Illumination of Integrated Analytical Systems

ABSTRACT

An analytical device including an optically opaque cladding, a sequencing layer including a substrate disposed below the cladding, and a waveguide assembly for receiving optical illumination and introducing illumination into the device. The illumination may be received from a top, a side edge, and a bottom of the device. The waveguide assembly may include a nanoscale aperture disposed in the substrate and extending through the cladding. The aperture defines a reaction cell for receiving a set of reactants. In various aspects, the device includes a sensor element and the illumination pathway is through the sensor element. Waveguides and illumination devices, such as plasmonic illumination devices, are also disclosed. Methods for forming and operating the devices are also disclosed.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. application Ser. No.13/895,486 filed May 16, 2013 which is a continuation of U.S.application Ser. No. 13/031,103 filed Feb. 18, 2011 which claimspriority to U.S. Provisional Application No. 61/306,235 filed Feb. 19,2010 and entitled INTEGRATED ANALYTICAL DEVICES AND SYSTEMS, U.S.Provisional Patent Application No. 61/387,916 filed Sep. 29, 2010 andentitled INTEGRATED ANALYTICAL SYSTEM AND METHOD, and U.S. ProvisionalPatent Application No. 61/410,189 filed Nov. 4, 2010 and entitledILLUMINATION OF INTEGRATED ANALYTICAL SYSTEMS, the entire contents ofwhich applications is incorporated herein for all purposes by thisreference.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH

Not Applicable.

BACKGROUND OF THE INVENTION

Analytical technologies continue to advance far beyond the test tubescale evaluations of the 19^(th) and 20^(th) centuries, and haveprogressed to the point where researchers can look at very specificinteractions in vivo, in vitro, at the cellular level, and even at thelevel of individual molecules. This progression is driven not just bythe desire to understand important reactions in their purest form, butalso by the realization that seemingly minor or insignificant reactionsin living systems can prompt a cascade of other events that couldpotentially unleash a life or death result.

In this progression, these analyses not only have become more focused onlesser events, but also have had to become appropriately more sensitivein order to be able to monitor such reactions. In increasing sensitivityto the levels of cellular or even single molecular levels, one mayinherently increase the sensitivity of the system to other non-relevantsignals, or “noise.” In some cases, the noise level can be of sufficientmagnitude that it partially or completely obscures the desired signals,i.e., those corresponding to the analysis of interest. Accordingly, itis desirable to be able to increase sensitivity of detection whilemaintaining the signal-to-noise ratio.

A large number of systems for optical analysis of samples or materialsemploy complex optical trains that direct, focus, filter, split,separate and detect light to and/or from the sample materials. Suchsystems typically employ an assortment of different optical elements todirect, modify, and otherwise manipulate light directed to and/orreceived from a reaction site.

Conventional optical systems typically are complex and costly. Thesystems also tend to have significant space requirements. For example,typical systems employ mirrors and prisms in directing light (e.g. laserlight) from its source to a desired destination. Additionally, suchsystems may include light splitting optics such as beam splitting prismsto generate two beams from a single original beam. In the case of modernanalysis systems, there is a continuing need for systems with very highthroughput and portability.

There is a continuing need for optical systems for creating morefocused, localized excitation signals. For example, analytical systemsfor monitoring processes at the single molecule level show great promisebut require illumination in a small volume. There is a need fordelivering a focused optical signal with specific characteristics toachieve the desired affect (e.g. excitation of single particles ofinterest). There is a continuing need for illumination devices andanalytical systems with reduced noise and improved performance.

There is a continuing need to improve upon the functionality, footprintand cost of systems for optical analysis. The present invention providesdevices, systems, and methods for overcoming the above problems inaddition to other benefits.

BRIEF SUMMARY OF THE INVENTION

The present invention is generally directed to an integrated analyticaldevice for analyses of a sample. A variety of elements may be integratedinto the device structure to enhance the performance and scalability ofthe device. Various aspects of the invention are directed to ananalytical system employing an integrated analytical device and elementsand methods for efficient integration.

Various aspects of the invention are directed to an analytical deviceincluding an optically opaque cladding layer, a sequencing layerincluding a substrate disposed below the cladding, and a waveguideassembly for receiving optical illumination and introducing illuminationinto the device. The illumination may be received from one of a top, aside edge, and/or a bottom of the device. The waveguide assembly mayinclude a nanoscale aperture disposed in the substrate and extendingthrough the cladding. The aperture defines a reaction cell for receivinga set of reactants.

Various aspects of the invention are directed to an analytical deviceincluding an optically opaque cladding layer, a sequencing layer, asensor element disposed in optical communication with the at least onenanoscale aperture along a detection pathway, and a waveguide forreceiving illumination and directing the illumination along anillumination pathway through the sensor element to the at least onenanoscale aperture for exciting a material of interest therein. Thesequencing layer may include a transparent substrate disposed below thecladding and at least one nanoscale aperture extending through thecladding to a top of the substrate, each aperture separated from anyother aperture by regions of the transparent substrate. In variousembodiments, part or all of the detection pathway is essentiallycoextensive with and opposite the illumination pathway.

Various aspects of the invention are directed to a system for monitoringanalytical reactions, the system including an analytical device having ananoscale reaction cell housing a set of reactants, the set of reactantsincluding an upconverting phosphor for receiving two or more photons ofa first energy level and emitting fewer photons of a second energy levelin response, the second energy level being greater than the first energylevel.

Various aspects of the invention are directed to a device for exciting afluorophore, the device including a first region having a reaction cellconfigured to receive a fluorophore, a second region laterally adjacentthe first region, the second region including a metal-insulator-metal(MIM) structure for providing plasmonic energy to the reaction cell, afourth region including an optical waveguide and inlet for receivingoptical energy, and a third region operationally positioned between thesecond region and the fourth region. In various embodiments, the thirdregion includes a transition portion at one end of the waveguideadjacent the MIM structure. In various embodiments, the transitionportion is dimensioned and configured to direct the received opticalenergy to the MIM structure thereby exciting surface plasmon polaritons(SPP) that are applied to the reaction cell.

Various aspects of the invention are directed to methods for forming andoperating the devices.

The methods and apparatuses of the present invention have other featuresand advantages which will be apparent from or are set forth in moredetail in the accompanying drawings, which are incorporated herein, andthe following Detailed Description of the Invention, which togetherserve to explain certain principles of the present invention.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a block diagram of an optical analytical device architecturein accordance with the present invention.

FIG. 2 is a schematic illustration of an integrated analytical device(optode) of the invention.

FIG. 3 is a schematic illustration of integration of an integratedanalytical device (optode) into an optode array chip in accordance withthe present invention.

FIG. 4 is a schematic view of a topside connection of fluidic andillumination elements to an integrated analytical device.

FIG. 5A is a schematic view a test socket and analytical system. FIG. 5Bis a perspective view of an exemplary test socket receiving an exemplaryanalytical optode chip.

FIG. 6 is a schematic view of a micro-pipette array for deliveringreagent to an optode chip array.

FIG. 7 is a cross-sectional view of the test socket and analyticalsystem illustrating microfluidic connections.

FIG. 8 is a schematic view of a top portion of the test socketillustrating distributed photonics and fluidics system.

FIG. 9 is a top view of a test socket of FIG. 8.

FIG. 10A-FIG. 10C show various layers in an optode array chip. FIG. 10Ais a layer having detectors and processing components, FIG. 10B is a topview of the device showing distributed fluidics and illuminationsystems. FIG. 10C shows the bottom of the device having electricalcontacts for connections with distributed power and signal systems.

FIG. 11 is a schematic view of an analytical device having directionalcomponents defining an optical guide path, the device being formed fromlayers on a substrate.

FIG. 12 is an exemplary plot of interleaved electrical data connectionsversus single molecule waveguides.

FIG. 13 is a schematic view of an array of reaction cells and theoptical emission profiles emanating from those reaction cells.

FIG. 14 is a schematic view of an array of reaction cells in atransparent substrate, illustrating an embodiment for providingillumination light to the reaction cells.

FIG. 15-FIG. 19 are several views of various devices and waveguidestructures configured for laser beam excitation in accordance with theinvention.

FIG. 20 is a cross-sectional view of an analytical device in accordancewith the invention, illustrating optical shielding pillars for shieldingthe zero mode waveguides.

FIG. 21-FIG. 23 are several views of various device and waveguidestructures configured for laser beam excitation in accordance with theinvention.

FIG. 24-FIG. 26 are several views of various integrated devices andpatterned waveguide structures in accordance with the invention.

FIG. 27 is a plot diagram of illustrating detector layer filtering usingthe downconverting tail technique in accordance with the invention.

FIG. 28 is a cross-sectional view of an analytical device in accordancewith the invention, illustrating use of notches and wedges for directingillumination light.

FIG. 29 is several views of methods of making analytical devices,illustrating various techniques and configurations for directingillumination light.

FIG. 30A-FIG. 30C show exemplary plots of interleaved excitationillumination and signal data using a system similar to that of FIG. 3.

FIG. 31 is a schematic view of a pixel design in accordance with theinvention.

FIG. 32 is a schematic illustration of one embodiment for exciting afluorophore.

FIG. 33 is a schematic view of a MJM structure in accordance with theinvention.

FIG. 34 is a schematic view of a waveguide assembly in accordance withthe invention for exciting a material with SPPs.

FIG. 35-FIG. 37 are several views of analytical devices configured forexcitation with surface plasmon polaritons.

FIG. 38 is a plot diagram of surface plasmon wavelengths based onincident photon energy for varying insulator thicknesses.

FIG. 39-FIG. 41 are several views analytical devices configured forexcitation with surface plasmon polaritons.

FIG. 42 is a schematic diagram of an analytical device with an array ofreaction cells and waveguides configured for measuring scattering fromnanoparticles.

DETAILED DESCRIPTION OF THE INVENTION

Reference will now be made in detail to the various embodiments of theinvention, examples of which are illustrated in the accompanyingdrawings. While the invention will be described in conjunction with thevarious embodiments, it will be understood that they are not intended tolimit the invention to those embodiments. On the contrary, the inventionis intended to cover alternatives, modifications and equivalents, whichmay be included within the spirit and scope of the invention as definedby the appended claims.

This application is related to U.S. Provisional Application No.61/306,235, filed Feb. 19, 2010 and entitled INTEGRATED ANALYTICALDEVICES AND SYSTEMS, the entire content of which is incorporated hereinfor all purposes by this reference.

I. Optical Analyses

The present invention is generally directed to improved systems, methodsand devices for use in optical analyses, and particularly, opticalanalyses of biological and/or chemical samples and reactions. Variousaspects of the invention are related to integrated devices and systemssuch as those described in U.S. Provisional Patent Application No.61/387,916, entitled INTEGRATED ANALYTICAL SYSTEM AND METHOD and filedon Sep. 29, 2010.

In various respects, the optical analyses of the invention generallyseek to gather and detect one or more optical signals, the appearance ordisappearance of which, or localization of which, is indicative of agiven chemical or biological reaction and/or the presence or absence ofa given substance within a sample material. In some cases, thereactants, their products, or substance of interest (all of which arereferred to as reactants herein) inherently present an opticallydetectable signal which can be detected. In other cases, reactants areprovided with exogenous labeling groups to facilitate their detection.Useful labeling groups include fluorescent labels, luminescent labels,mass labels, light scattering labels, electrochemical labels (e.g.,carrying large charge groups), metal labels, and the like. Exemplars ofsuch labeling groups are disclosed by U.S. Pat. No. 7,332,284 and U.S.Patent Publication Nos. 2009/0233302 filed Mar. 12, 2009, 2008/0241866filed Mar. 27, 2008, and 2010/0167299 filed Nov. 17, 2009, the contentsof which patents and applications are incorporated herein for allpurposes by this reference.

In various embodiments, one or more reactants in an analysis is providedwith a fluorescent labeling group that possesses a fluorescent emissionspectrum that is shifted from its excitation spectrum, allowingdiscrimination between the excitation light source and the emission ofthe label group. These fluorescent labels typically have high quantumyields, further enhancing their detectability. A variety of differentfluorescent label groups are well known in the art, and includefluorescein and rhodamine based organic dyes, such as those sold underthe Cy3 and Cy5 labels from, e.g., GE Healthcare, and the AlexaFluor®dyes available from Life Technologies, Inc. A wide variety of organicdye structures have been previously described in the art.

Other fluorescent label groups include, for example, particle-basedlabeling groups. Some such particle label groups constitute encapsulatedor otherwise entrained organic fluorophores, while others comprisefluorescent nanoparticles, such as inorganic semiconductor nanocrystals,e.g., as described in U.S. Pat. Nos. 6,207,392, 6,225,198, 6,251,303,6,501,091, and 7,566,476, the full disclosures of which are incorporatedherein by reference in their entirety for all purposes.

“Nano-scale” and “micro-scale” are to be understood as generally used inthe analytical arts and physics. As used herein, however, the term“nano-scale” may include dimensions slightly larger or smaller than“nano-scale.” In various respects, “nano” and “micro” are generallyoverlapping. For example, “nano-scale aperture” may refer to an aperturehaving dimensions on either the nano- or micro-scale. Similarly,“microfluidics” is not intended to limit the fluidic devices to themicro-scale. One will appreciate that the size and dimensions of theelements may vary depending on the application.

By detecting these fluorescent labeling groups, one can ascertain thelocalization of a given labeled reactant, or detect reaction events thatresult in changes in the spectral or other aspects of the fluorescentlylabeled reactant. For example, in binding or hybridization reactions,the ability of a labeled reactant to bind to another immobilizedreactant is detected by contacting the reactants, washing unboundlabeled reactant away, and observing the immobilized reactant to lookfor the presence of bound fluorescent label. Such assays are routinelyemployed in hybridization assays, antibody assays, and a variety ofother analyses.

In a number of different nucleic acid sequencing analyses,fluorescently-labeled nucleotides are used to monitor thepolymerase-mediated, template-dependent incorporation of nucleotides ina primer extension reaction. In particular, a labeled nucleotide isintroduced to a primer template polymerase complex, and incorporation ofthe labeled nucleotide is detected. If a labeled nucleotide isincorporated, it is indicative of the underlying and complementarynucleotide in the sequence of the template molecule. In traditionalSanger sequencing processes, the detection of incorporation of labelednucleotides utilizes a termination reaction where the labelednucleotides carry a terminating group that blocks further extension ofthe primer. By mixing the labeled terminated nucleotides with unlabelednative nucleotides, one generates nested sets of fragments thatterminate at different nucleotides. These fragments are then separatedby capillary electrophoresis, to separate those fragments that differ bya single nucleotide, and the labels for the fragments are read in orderof increasing fragment size to provide the sequence (as provided by thelast-added, labeled terminated nucleotide). By providing a differentfluorescent label on each of the types of nucleotides that are added,one can readily differentiate the different nucleotides in the sequence(e.g., U.S. Pat. No. 5,821,058, incorporated herein for all purposes bythis reference).

In newer generation sequencing technologies, arrays of primer-templatecomplexes are immobilized on surfaces of substrates such that individualmolecules or individual and homogeneous groups of molecules arespatially discrete from other individual molecules or groups ofmolecules, respectively. Labeled nucleotides are added in a manner thatresults in a single nucleotide being added to each individual moleculeor group of molecules. Following the addition of the nucleotide, thelabeled addition is detected and identified.

In some cases, the processes utilize the addition of a single type ofnucleotide at a time, followed by a washing step. The labelednucleotides that are added are then detected, their labels removed, andthe process repeated with a different nucleotide type. Sequences ofindividual template sequences are determined by the order of appearanceof the labels at given locations on the substrate.

In other similar cases, the immobilized complexes are contacted with allfour types of labeled nucleotides where each type bears adistinguishable fluorescent label and a terminator group that preventsthe addition of more than one nucleotide in a given step. Following thesingle incorporation in each individual template sequence (or group oftemplate sequences,) the unbound nucleotides are washed away, and theimmobilized complexes are scanned to identify which nucleotide was addedat each location. Repeating the process yields sequence information ofeach of the template sequences. In other cases, more than four types oflabeled nucleotides are utilized.

In particularly elegant approaches, labeled nucleotides are detectedduring the incorporation process, in real time, by individual molecularcomplexes. Such methods are described, for example, in U.S. Pat. No.7,056,661, which is incorporated herein by reference in its entirety forall purposes. In these processes, nucleotides are labeled on a terminalphosphate group that is released during the incorporation process so asto avoid accumulation of label on the extension product and avoid anyneed for label removal processes that can be deleterious to thecomplexes. Primer/template polymerase complexes are observed during thepolymerization process, and nucleotides being added are detected byvirtue of their associated labels. In one particular aspect, they areobserved using an optically confined structure, such as a zero modewaveguide (e.g., U.S. Pat. No. 6,917,726, which is incorporated hereinby reference in its entirety for all purposes) that limits exposure ofthe excitation radiation to the volume immediately surrounding anindividual complex. As a result, only labeled nucleotides that are inthe process of being incorporated are exposed to excitation illuminationfor a time that is sufficient to identify the nucleotide. In anotherapproach, the label on the nucleotide is configured to interact with acomplementary group on or near the complex, e.g., attached to thepolymerase, where the interaction provides a unique signal. For example,a polymerase may be provided with a donor fluorophore that is excited ata first wavelength and emits at a second wavelength, while thenucleotide to be added is labeled with a fluorophore that is excited atthe second wavelength but emits at a third wavelength (e.g., U.S. Pat.No. 7,056,661, previously incorporated herein). As a result, when thenucleotide and polymerase are sufficiently proximal to each other topermit energy transfer from the donor fluorophore to the label on thenucleotide, a distinctive signal is produced. Again, in these cases, thevarious types of nucleotides are provided with distinctive fluorescentlabels that permit their identification by the spectral or otherfluorescent signature of their labels.

As will be appreciated, a wide variety of analytical operations may beperformed using the overall reaction framework described herein and areapplicable to the present invention. Such reactions include reactiveassays, e.g., examining the combination of reactants to monitor the rateof production of a product or consumption of a reagent, such as enzymereactions, catalyst reactions, etc. Likewise, associative or bindingreactions may be monitored where one is looking for specific associationbetween two or more reactants, such as nucleic acid hybridizationassays, antibody/antigen assays, coupling or cleavage assays, and thelike.

II. Analytical Device

The analytical system in accordance with the present invention employsone or more analytical devices referred to as “optode” elements. In anexemplary embodiment, the system includes an array of analytical devicesformed as a single integrated device. An exemplar of a suitable optodeelement is disclosed by U.S. Provisional Application No. 61/306,235filed on Feb. 19, 2010, and entitled INTEGRATED ANALYTICAL DEVICES ANDSYSTEMS (the '235 application), the entire contents of which areincorporated herein for all purposes by this reference. The exemplaryarray is configured for single use as a consumable. In variousembodiments, the optode element includes other components including, butnot limited to, local fluidics, electrical connections, a power source,illumination elements, detector elements, logic, and a processingcircuit. Each analytical device or array is configured for performing ananalytical operation as described above.

While the components of each device and the configuration of the devicesin the system may vary, each analytical device typically comprises thegeneral structure shown as a block diagram in FIG. 1. As shown, ananalytical device 100 typically includes a reaction cell 102, in whichthe reactants are disposed and from which the detector optical signalsemanate.

“Reaction cell” is to be understood as generally used in the analyticaland chemical arts and refers to the location where the reaction ofinterest is occurring. Thus, “reaction cell” may include a fullyself-contained reaction well, vessel, flow cell, chamber, or the like,e.g., enclosed by one or more structural barriers, walls, lids, etc., orit may comprise a particular region on a substrate and/or within a givenreaction well, vessel, flow cell or the like, e.g., without structuralconfinement or containment between adjacent reaction cells. The reactioncell may include structural elements to enhance the reaction or itsanalysis, such as optical confinement structures, nanowells, posts,surface treatments such as hydrophobic or hydrophilic regions, bindingregions, or the like.

In various respects, “analytical device” refers to a reaction cell andassociated components that are functionally connected. In variousrespects, “analytical system” refers to one more associated analyticaldevices and associated components. In various respects, “analyticalsystem” refers to the larger system including the analytical system andother off-chip instruments for performing an analysis operation such asa power source and reservoir.

In some cases, one or more reactants for the reaction of interest may beimmobilized, entrained or otherwise localized within a given reactioncell. A wide variety of techniques are available for localization and/orimmobilization of reactants including surface immobilization throughcovalent or non-covalent attachment, bead, or particle-basedimmobilization, followed by localization of the bead or particle,entrainment in a matrix at a given location, and the like. Reactioncells may include ensembles of molecules, such as solutions or patchesof molecules, or it may include individual molecular reaction complexes,e.g., one molecule involved in the reaction of interest as a complex.Similarly, the overall devices and systems of the invention may includeindividual reaction cells or may comprise collections, arrays, or othergroupings of reaction cells in an integrated structure, e.g., amultiwell or multi-cell plate, chip, substrate or system. Some examplesof such arrayed reaction cells include nucleic acid array chips, e.g.,GeneChip® arrays (Affymetrix, Inc.), zero mode waveguide arrays (asdescribed elsewhere herein), microwell and nanowell plates, multichannelmicrofluidic devices, e.g., LabChip® devices (Caliper Life Sciences,Inc.), and any of a variety of other reaction cells. In variousrespects, the “reaction cell”, sequencing layer, and zero modewaveguides are similar to those described in U.S. Pat. No. 7,486,865 toFoquet et al., the entire contents of which is incorporated herein forall purposes by this reference.

Although the exemplary analytical system includes an array of analyticaldevices having a single waveguide layer and reaction cell layer, onewill appreciate that a wide variety of layer compositions may beemployed in the waveguide array substrate and cladding/reaction celllayer and still achieve the goals of the invention (e.g., published U.S.Patent Application No. 2008-0128627, incorporated herein for allpurposes by this reference).

The analysis system typically includes one or more analytical devices100 having a detector element 120, which is disposed in opticalcommunication with the reaction cell 102, that is, the detector elementis configured for direct detection of an emission event within thereaction cell. One will appreciate that such optical communication mayinclude radiative or non-radiative communication. Optical communicationbetween the reaction cell 102 and the detector element 120 may beprovided by an optical train 104 comprised of one or more opticalelements generally designated 106, 108, 110 and 112 for efficientlydirecting the signal from the reaction cell 102 to the detector 120.These optical elements may generally comprise any number of elements,such as lenses, filters, gratings, mirrors, prisms, refractive material,or the like, or various combinations of these, depending upon thespecifics of the application.

In various embodiments, the reaction cell 102 and detector 120 elementare provided along with one or more optical elements in an integrateddevice structure. By integrating these elements into a single devicearchitecture, one improves the efficiency of the optical couplingbetween the reaction cell and the detector. In particular, inconventional optical analysis systems, discrete reaction vessels aretypically placed into optical instruments that utilize free-space opticsto convey the optical signals to and from the reaction vessel and to thedetector. These free space optics tend to include higher mass and volumecomponents, and have free space interfaces that contribute to a numberof weaknesses for such systems. For example, such systems have apropensity for greater losses given the introduction of unwanted leakagepaths from these higher mass components, and typically introduce higherlevels of auto-fluorescence, all of which reduce the signal to noiseratio (SNR) of the system and reduce its overall sensitivity, which inturn can impact the speed and throughput of the system. Additionally, inmultiplexed applications, signals from multiple reaction regions (i.e.,multiple reaction cells or multiple reaction locations within individualcells) are typically passed through a common optical train, or commonportions of an optical train, using the full volume of the opticalelements in that train to be imaged onto the detector plane. As aresult, the presence of optical aberrations in these optical components,such as diffraction, scattering, astigmatism, and coma, degrade thesignal in both amplitude and across the field of view resulting ingreater noise contributions and cross talk among detected signals.

The devices of the invention, in contrast, include relatively lowvolumes between the reaction cell and the detector, thereby reducing thenoise contributions from those components and provide few or no freespace interfaces that can contribute to the noise profile of the systemthrough the introduced reflections and losses from large index changesfrom the components to air or free space. Further, in preferred aspects,a given reaction region is provided with its own devoted optical trainto direct signals to a devoted portion of the sensor.

In various embodiments, the device is configured such that emitted lightfrom the fluorescent species in the nanoscale well is not transmittedthrough free space. By “not transmitted through free space” it isgenerally meant that the respective element (e.g. a signal or energy) isnot transmitted through open space or free space optics, and in variousrespects, is transmitted only through light-modulating media. Suchlight-modulating media may include refractive devices such as an opticallens that makes use of the refractive index of a defined volume of air.By contrast, light-modulating media generally does not include ambientair open to the environment.

As a result of the integrated architecture, optical aberrations areconfined to individual reaction regions as opposed to being appliedacross an entire array of reaction regions. Likewise, in a furtheraspect, the reaction region, optical train, and detector are fabricatedin an integrated process, e.g., micromechanical lithographic fabricationprocesses so that the components are, by virtue of the manufacturingprocess, pre-aligned and locked into such alignment by virtue of thefabrication process. Such alignment is increasingly difficult using freespace optics systems as reaction region sizes decrease and multiplexincreases. In addition, by integrating such components into one unifiedcomponent, relative movement between such sub-components, as is the casewith free space optics, can make drift and continued alignment resultingfrom vibrations a more difficult task. Likewise, the potential forcontamination in any of the intermediate spaces (e.g. dust and othercontaminants), is eliminated (or at least substantially reduced) in anintegrated system as compared to free space systems.

In addition to reducing noise contributions from the optical pathway,the integrated devices of the invention also benefit from fabricationprocesses and technology that eliminate other issues associated withdiscrete reaction cell, optic, and detection components. For example,with respect to certain highly multiplexed or arrayed reaction cells,initial alignment and maintaining alignment of the detection with thereaction cell over the full length of the analysis can raisedifficulties. This is particularly the case where excitationillumination may be specifically targeted among different arraylocations of the reaction cell and/or among different reaction cells.

In the embodiment shown in FIG. 1, a signal source, a transmission layercomprising optical components to modulate the light transmittedtherethrough, and a detector are joined together into an integrateddevice.

As used herein, the term “integrated” may have different meanings whenused to refer to different aspects of the invention. For example, in thecase of an integrated device or an integrated optical system, the term“integrated” generally means that the various components are physicallyconnected, and that the optical signals pass from component to componentwithout passing into air or free space, as would be understood by one inthe field of optics. In the context of the description of a system, theterm “integrated” is to be understood as generally used in theanalytical and electrical engineering fields, where “integrated” wouldrefer, for example, to a combination or coordination of otherwisedifferent elements to provide a harmonious and interrelated whole,whether physically or functionally. The meaning of the term willgenerally be understood by one of skill in the art by the context inwhich it is used.

Being an integrated device, the light emitted from the reactor cell 102will pass through to the detector without passing through air or freespace. In some embodiments, the integrated analytical device alsocomprises components for providing illumination to the reactor cell 102.For example, in many cases where reactor cell 102 comprises a zero modewaveguide, it is often desirable to provide illumination from below thereactor cell, for example between the bottom of reactor cell 102 and thetransmission layer or optical train 104. In some cases, a waveguidestructure is incorporated into the analytical device to provide suchillumination. Analytical devices comprising waveguides for illuminationare described in more detail herein, and for example, in U.S. patentapplication Ser. No. 11/849,157 filed Aug. 31, 2007 and Ser. No.12/560,308 filed Sep. 15, 2009, which are incorporated herein byreference for all purposes.

In various embodiments, the analytical device is a substrate including areaction cell array, and a detector array on a bottom surface of thearray. The device may also include other components such as processingcircuits, optical guides, and processing circuits. In variousembodiments, the analytical device may be formed by building layers on asubstrate or by bonding two or more substrates. In an exemplary device,a fused silicon (FuSi) substrate, a ZMW layer, and a silicon substratewith a photodetector array are bonded together to form the array ofanalytical devices. One will appreciate that such integrated analyticaldevices have significant advantages in terms of alignment and lightcollection. For example, the reaction site and detector are alignedthrough the manufacturing process. One will appreciate from thedescription herein, that any of the components and systems may beintegrated or modified in various manner. In another example, the ZMWsubstrate and detector array are on separate substrates that are broughttogether for the experiment, after which the ZMW substrate is replacedwith another substrate for a second experiment. With this approach, thedetector array may be re-used rather than being disposed with the ZMWsubstrate after an experiment. It may also be more cost effective as theyields from each of the processes are separated. In this manner, the ZMWarray and detector array are in intimate contact during the experiment(as if they are part of an integrated device), but they can be separatedafter the measurement.

The size of the processing circuits in each of the analytical devicesmay be minimized to reduce costs. By developing a board in the receivercamera electronics (e.g. massively parallel DSP or microprocessor or adedicated FPGA, CPLD or ASIC), overall operating costs (i.e.$/mega-base) may be minimized.

Another embodiment of an integrated analytical device of the invention(optode) is shown in FIG. 2. While FIG. 2 is shown in open form toillustrate the various components, it is to be understood thatanalytical device of FIG. 2 represents a structure that comprises allsolid or liquid components and that there is no open space between thecomponents.

The analytical device has a reaction cell 802 that is coupled with areagent reservoir or fluid conduit 806 which delivers reactants to thereaction cell 802. The reaction cell can be a nanoscale well or zeromode waveguide. In some cases, the reaction cell will have a biomoleculesuch as a polymerase enzyme immobilized within it. The fluidic conduitcan provide reagents across a number of reaction cells. Below thereaction cell is a waveguide for providing excitation illumination tothe reagents within the reaction cell. While a waveguide is shown here,other optical elements such as those provided elsewhere herein can beused to provide light from under the reaction cell. The illuminationlight can be used to excite fluorescent emission from reagents with thereactor cell. The light emitted from the reaction cell is directeddownward through a transmission layer, which acts to transmit the lightfrom the reaction cell to the detector. In some cases, the transmissionlayer will have optical components to enhance the efficiency of thelight transfer or modulate the light. In the analytical device of FIG.2, an optical tunnel or conduit 808 is disposed in optical communicationwith the reaction cell 802, which is in turn in optical communicationwith sensing element(s) 810 in the detector. In some cases, the detectorhas multiple sensing elements, each for detecting light having adifferent color spectrum. For example, in the case of sequencing, thesensor for each reaction cell can have 4 elements, one for each of thefour bases. In some cases the sensor elements provide colordiscrimination, in other cases, color filters are used to direct theappropriate color of light to the appropriate sensor element shown as amulticolor discriminating set of sensor elements in FIG. 2. The sensorelements are coupled to appropriate electronic components 812, such asbusses and interconnects, that make up the overall sensor or camera. Theelectronic components can also include processing elements forprocessing the signal from the detectors.

III. Optode Arrays and Packaging

The integrated analytical devices of the invention are generallyfabricated into arrays of devices, allowing for simultaneously observingthousands to millions of analytical reactions at one time. These arraysof optodes generally require the input of fluids to provide reagents andthe conditions necessary for carrying out analytical reactions, theinput of excitation light for the measurement of fluorescence, andconnections for the output of signal data from the detectors. Theinvention provides devices, systems, and methods for packaging theoptode arrays for these inputs and outputs.

FIG. 3 provides an embodiment for providing an array of optode elementsinto an optode array group and an optode array chip, which facilitatethe input of light and fluid and the electronic output of data. Theoptode array chip can be introduced into an instrument or system that isconfigured with the required input and output connections. For example,in some cases the light and fluid can be introduced from above throughinput ports on the top of the chip, and electronic data can be extractedfrom below the chip from electronic contacts on the bottom of the chip.The optode array group comprises an optode array component 310, afluidic input component 320, and an illumination input component 330. Inthe embodiment shown in FIG. 3, the fluidic input component 320 andillumination input component 330 are attached to the optode arraycomponent at the edges.

The exemplary optode array component 310 comprises an array of optodeelements. The number of optodes in the array can be set by thecharacteristics of the analytical reaction to be measured. The number ofoptode elements in an optode array component can be from about 10 toabout a million or more. In some cases the number of optode elements isfrom about 100 to about 100,000. As shown in FIG. 3, the fluidic conduitextends over a given optode to the optodes on other sides. As shown inthe figure, the exemplary fluidic conduit extends across the optodeelement in one direction, but essentially not in the perpendiculardirection. The fluidic conduits can be fashioned in some cases to extendover multiple optode elements in either or both directions. In somecases, the conduit can deliver fluid to all of the optodes on the optodearray component. In some cases, one conduit can deliver fluid to asubset of the optode elements, while other conduits deliver fluid toother optode elements. In some cases, each conduit delivers fluid to asingle optode element. Analogously, the waveguides shown for a singleoptode element in the figure generally extend across multiple optodeelements in the array. The waveguides can be channel waveguidesextending down a single row of optode elements providing illumination tothe reaction cells in that row, or the waveguides can be channelwaveguides wider than one row, illuminating more than one row. Thewaveguides can also be planar waveguides illuminating sections orilluminating all of the reaction cells in the optode array component.

The fluidic input component 320 has a fluid input port 322 forintroduction of fluids to the optode array chip. In the embodiment shownin FIG. 3, the fluid input port is accessible from the top. The fluidicinput port 322 has a number of fluidic conduits that extend from theinput port to the optode array component. The fluidic conduits on thefluidic input port generally mate directly with the fluidic conduits onthe optode array component, and both components are generally formed inthe same set of process steps. The number of fluidic conduits may dependon the application. In some cases, one fluidic conduit will providefluid for one row within the reaction cells in the optode arraycomponent.

The illumination input component 330 has an illumination input port 332such as a light pipe for the input of illumination light onto the optodearray chip. The illumination input port 332 is connected to a pluralityof waveguides that extend from the illumination input port into thewaveguides on the optode array. Briefly, waveguides may be providedwithin the substrate by including higher IR regions to convey lightthrough a lower IR material substrate, where the lower IR materialfunctions as a partial cladding for the waveguide. The waveguide meetsthe reaction cell with an absence of cladding, allowing evanescentillumination of the reaction cell from the waveguide.

The combination of an optode array component 310, a fluidic inputcomponent 320, and an illumination input component 330 as shown in FIG.3 can be referred to as an optode array group. A plurality of optodearray groups can be combined to form an optode array chip. The optodearray chip can comprise from 1 to about 100, from about 100 to about1,000, or more optode array groups. The optode array chip comprisingmultiple optode array groups can be fabricated using semiconductor andmicrofabrication processing techniques. For example, an optode arraychip containing an array of optode array groups can be fabricated on awafer, and the wafer can be diced into smaller optode array chips havingthe appropriate number of optode array groups for a particularapplication. The optode array chips thus produced will have the fluidicand illumination input ports, and will have electrical contactsextending from the detectors and other electronic elements on the chipfor the transfer of data.

FIG. 4 illustrates how an optode array component (middle) having, forexample, 200 by 200 optode elements can be supplied with fluid and lightfrom the side. Fluidic port 33 c dispenses fluid into an array offluidic channels that bring the fluid to the reaction cells or ZMWs.Light pipe 53 couples light into channels that transfer the illuminationlight into the reaction cells from below. Emitted light from the ZMWs istransmitted through a transparent transmission layer down to thedetector, in this case a photodiode. The photodiodes detect opticalsignals and transmit data signals into image processing elements on thechip. Processed signal data is sent to computers for further processingthrough the electrical contacts on the bottom of the chip.

In one aspect, the invention comprises a device comprising an array ofoptode elements wherein each optode element has a reaction cell such asa ZMW or a nanoscale aperture within a cladding layer, the reaction cellconfigured to receive fluid that contains the reactive species to beanalyzed. The analysis generally comprises at least one fluorescentlylabeled species, the fluorescence from which will provide informationabout the reaction. Above the reaction cell is a fluidic layer that isin fluid communication with the reaction cell. Below the aperture layeris a waveguide layer that provides illumination to the nanoscale wellwith evanescent irradiation. The waveguide layer can comprise channelwaveguides and/or planar waveguides. Below the waveguide layer is atransmission layer that transmits light emitted from the fluorescentspecies in the reaction cell to the detector below. Below thetransmission layer is a detector layer which receives and detects theemitted light transmitted through the transmission layer, wherein theemitted light is transmitted to the detector without being transmittedthrough air. In some cases, the detector layer has below it electricalcontacts for transmitting data signals out of the chip into computercomponents for analysis and processing. In some cases processingelements are built into the chip to provide some processing of thesignals before sending the data off of the chip.

The array of optode elements is generally provided in one integrated,solid package. In some cases, the portion of the array of optodeelements that comprise the detector can be reversibly separated from theportion of the array comprising the reaction cell. This allows for thedetector portion to be used over and over again with different arrays ofreaction cells.

IV. Measurement Systems Comprising Optode Arrays

The optode array chips comprising optode arrays, inputs for light andfluid, and outputs for electronic transfer of data can be inserted intostructures that provide for the analysis reaction. In some cases, theoptode array chip can be sandwiched within an assembly that providesphysical alignment of the input and output features, and can provide theforce required for effective mating of the assembly components. Oneapproach to an assembly is the use of a clamshell assembly. An exemplarysystem includes an array of analytical devices integrated into a systemwith a test socket. An exemplary system architecture makes use ofautomated testing equipment and chip-scale packaging techniques. Invarious embodiments, the test socket is an automated test equipment(ATE) socket (shown in FIG. 5A). In the exemplary system, the socket isconnected to the processing system and other system components such asthe electrical system.

In some aspects the invention provides an assembly having a sandwichstructure comprising: a top piece comprising inputs for illuminationlight and fluid; an integrated analysis chip in the middle comprising:an aperture layer comprising a plurality of nanoscale apertures througha cladding layer in fluidic contact with the top of the chip, and awaveguide layer comprising a plurality of waveguides configured toprovide illumination light to the nanoscale apertures from below, thewaveguide layer having one or more illumination ports on the top surfacefor providing illumination light to the waveguides; a transmission layercomprising a transparent material for transmitting emitted light fromthe nanoscale apertures; a detector array layer below the transmissionlayer having detectors electrically connected to pins extending out thebottom of the chip; and a bottom piece having electrical contactscorresponding to the pins on the bottom of the chip; the assemblyconfigured such that upon closure, the chip is aligned with the top andbottom pieces to allow input of the illumination light and fluid fromthe top piece and extraction of electrical signals from the bottompiece.

An exemplary integrated device isolates the electrical components fromthe optical and fluid components, for example, having the optical andfluid delivery on one side and the electrical interconnects on the otherside of the device. One embodiment of a system is shown in FIGS. 5 and5A in which an optode array chip 40 comprising, for example, an array ofoptode array groups 56, is inserted into a socket comprising a top piece51 which delivers illumination through an illumination system 53 andfluidics delivery system 33 to the optode array chip, and bottom piece57 which has an array of electrical contacts which mate with theelectrical contacts on optode array chip. In some embodiments the socketcan use vacuum to pull the components of the system together to enhancefluidic, illumination, and electrical contacts.

The electrical connections are generally on the bottom surface of theintegrated device and optical and fluidic connections on the top side ofthe device (shown in FIG. 5). The partition of the electrical andoptical components in this exemplary manner provides for a two-sidedsocket that can supply all 110 connections within standard commercialtolerances. As an example, the clamshell socket used in the exemplarycommercial ATE may be modified to be used with the analytical array 40.Such test sockets generally have over 50,000 insertion cycle reliabilityand provide adequate and uniform contact force. Moreover, because thecomponents are integrated into a single device and the socket isself-seating, the optical components and detector are automaticallyaligned. The exemplary includes spring loaded durable contact pins andoxide scrubbing crowns to further promote auto alignment and reliablecontact. Thus, the integrated device can be easily connected to theprocessing system and other system components by insertion into thesocket. This provides higher reliability, lower cost, and generallyeasier use by the technician.

The reagent handling, sample handling, and illumination functions may beperformed in a distributed manner on an area above a processing regionof the integrated device and adjacent to the reactor cells. Theillumination ports and fluidics ports may be positioned in alternatingrows in a checkerboard pattern. These illumination and fluidic ports canservice either a single adjacent optode array component 56 or in somecases can service four of the nearest neighboring optode arraycomponents. The distribution of illumination and fluids is more uniform,less complex, and performance is maintained to very high multiplex viaarray segment scalability. Each array segment illumination and fluidicscan be individually controlled if desired. In various embodiments,fluidics and photonic connections to socket 51 are made on the topportion of device 40.

With the illustrated top-bottom connection set-up, a standard clamshellpackaging technique (e.g. ATE socket) as described above can be used toconnect the device to the overall system. As shown in FIG. 4, forexample, the topside connections involve the alignment of multipleillumination light pipes 53 and microfluidic nozzles 33. For example, ifa 2000×2000 cell array is needed and 100 array segments are placed in200×200 multiplex on 5 micrometer centers, the adjacent 100 I/O andprocessing segments are 1 mm×1 mm in size. Therefore, 10×5 connectionsof both illumination and fluidics are needed but have achievablealignment at the pitches described. In a similar fashion, the datareduction performed in the processing regions reduces the number ofelectrical connections that need to be interfaced to the externalcircuitry. Standard electrical bump bonds can be used to connect withstandard durable electrical sockets with achievable tolerances for highspeed operation. The light pipe 53 in the system of FIG. 4 is configuredto direct a light signal distributed over the device to a site ofinterest, in the exemplary case, a waveguide. The integrated waveguidethen directs the light to respective reaction cells.

Referring to FIG. 5, a sample is provided to the top of the socket andintroduced to a set of pipettes that are aligned with the fluidic portson the optode array. Since the optodes are grouped into sub-arrays, thereduced number of fluidic ports allows for alignment to standardcommercial tolerances (e.g. about 0.3 mm) and the reduced number ofconnections increases reliability. The failure of a single port does notmake the entire experiment invalid and the remaining ports can collectdata.

The integrated system of the present invention is typically configuredto introduce fluids and optical signals. To provide for a sterileenvironment to introduce sample and reagent, a low cost fluidicdistribution device with single-use capability can be inserted into thesocket with each experiment. This fluidic device can be molded withstandard bio-compatible polymers similar to multiple micro-pipettesystems sold by companies such as Biohit, Thermo and Eppendorf. Anexample of a disposable 2-D micro-pipette insert for the ATE clamshellsocket lid is shown in FIG. 6. FIG. 7 shows a diagram of theintroduction of fluids into the optode array chip with an array ofmicropipettes configured to mate with the fluidic input ports on anoptode array chip. The micropipette array 83 mates with fluidic inputports 82 on the optode array chip. The fluid extends down conduits 86into the optode elements. The ZMWs within the optode elements areilluminated, and emitted light is transmitted through light pipes to thedetectors 84. The detectors send signals to data processing componentswithin the chip.

The introduction of fluidics to optode groups may be done withhomogenous material, or alternatively, each optode group could beoperated with a different sample or reagent setup to perform highlymultiplexed assay experiments. The temperature of each fluidic input canalso be adjusted or maintained, for example, to provide variability inthe assay.

In various embodiments, the introduction of the photonic illuminationsignal is accomplished with discrete light ports at the top part of theclamshell socket within commercial tolerances (e.g. between about 0.3 mmto about 0.6 mm). By distributing the light energy in the durable socketto local optode regions, careful design and exotic materials can be usedto minimize losses, enable polychromatic excitation and reduce heat loadon the active single use device. For example, a lithium niobatewaveguide structure can be designed with very low insertion andpropagation losses to the optode group. Lower quality distributionnetworks on the disposable chip are enabled as the transmission distanceand branching are significantly reduced. The photonic distributionnetwork can be developed to be interleaved with the microfluidicdistribution insert as shown in FIG. 8 and FIG. 9.

Turning to FIGS. 10A, 10B, and 10C, an array with distributed functionsis shown. FIGS. 10A, 10B, and 10C represent layers within an optodearray chip illustrating the various functions performed in differentportions of the chip. The exemplary optode array chip includes aplurality of individualized analytical devices for carrying out areaction. FIG. 10B shows the topside of the optode array chip havingreactor array components 71, illumination input components 72, andfluidic input components 73. FIG. 10A shows the layer in which theoptode array components have an array of detectors 70. As illustrated,the detectors are connected to processing components 75. Theseprocessing components process the signal from the detectors beforesending the signal on for further processing and analysis. FIG. 10Cshows the base of the optode array chip. The base has an array ofelectrical connections. In the embodiment shown, the portions of thechip under the optode array components have contacts for the input ofpower. The portions of the chip under the fluidic input and illuminationinput components have electrical contacts for the output of signal fromthe signal processing elements. The exemplary optode array chip isconfigured for efficient processing. Some of the functions, such asdetection, are carried out within each optode. Other functions arehandled by groups of optodes or across the distributed system. Forexample, the fluidics system extends across the rows and columns ofoptodes.

The illustrated array is manufactured using techniques similar tosilicon wafer preparation and testing techniques. The array is built upfrom a substrate with any of the above mentioned analytical elements.The array does not require regular spacing. One will further appreciatethat the system architecture can be easily set up and scaled. Each“unit” may be an integrated, local system with a number of optical,detection, and processing elements. The outputs of each of the reactorcell detectors (containing the preprocessed pixel data) is connected toa processing circuit where many functions of various utilities can beperformed including, but not limited to, data reduction, digitization,buffer storage, bus arbitration, and the like.

Referring to FIG. 10B, the reagent handling and illumination can beperformed in a distributed manner using the area above the processingregion and adjacent to each of the respective reactor cells. Acheckerboard pattern of alternating rows of illumination ports andfluidics ports is provided. These fluidic and illumination ports can beprovided as described above as arrays of optode array groups. Theseports can service either the single adjacent reactor array or aplurality of arrays. In various embodiments, each node or set of portsservices the neighboring arrays (e.g. arrays on each of the four sides).In contrast to conventional devices, the distribution of illuminationand fluids is more uniform and less complex and performance ismaintained to very high multiplex via array segment scalability. Onewill appreciate that each array segment illumination and fluidics can beindividually controlled if desired.

Referring to FIG. 10C, the readout of array segments can be performedvia local through-hole vias to substrate connections. The packaging andtesting of the system can be done with industry accepted and verifiedprocesses. To complement the fluidic and illumination connections on thetopside of the wafer, a number of electrical connections representingthe I/O of the array segments may be made on the bottom of the wafer asdiscussed above. These connections can be segmented by power and signalgroups. Thus, the connections are positioned at the top and bottom ofthe array chip.

A standard clamshell packaging technique (e.g. ATE socket) as describedabove can be used to connect the chip device to the overall system. Asshown in FIG. 4, for example, the topside connections involve thealignment of multiple illumination light pipes 53 and microfluidicnozzles 33. For example, if a 2000×2000 cell array is needed and 100array segments are placed in 200×200 multiplex on 5 micrometer centers,the adjacent 100 I/O and processing segments are about 1 mm×1 mm insize. Therefore, 10×5 connections of both illumination and fluidics areneeded but have achievable alignment at the pitches described. In asimilar fashion, the data reduction performed in the processing regionsreduces the number of electrical connections that need to be interfacedto the external circuitry. Standard electrical bump bonds can be used toconnect with standard durable electrical sockets with achievabletolerances for high speed operation.

In some embodiments, a plurality of devices are formed in a substrate(e.g. wafer) cut from a sheet material. The wafer can comprise, forexample, silicon or fused silica. The exemplary device includes areal-time sensing structure integrated with the chemical reaction cellsand provides for the decoupling of the reactor location with the opticalelements. The detector elements are grouped around distributedprocessing cells thereby enabling significant performance advantageswith high parallelism. In addition, this architecture reduces thedistribution path for fluidics, signal, and stimulus by arranging cellsinto groups of manageable I/O “pads” corresponding to optode groups.

The implementation of integrated sensing elements with the cellarrays/reactors provides many benefits including higher speed operationand the ability to extract tagged signals from reduced emissions withsynchronized light. FIG. 11 shows another embodiment of an integratedanalytical device cell with a fully contained light source, cell reactorelement, and detector. By eliminating common and redundant illuminationand detection paths, the fidelity of the sensed signal is maintained.

While there are many benefits of a distributed architecture, thedistribution branching network required for a high resolution arraypresents some challenges and limitations. For example, the lossesassociated with a waveguide operating with many branches and taps willintroduce a light intensity gradient across the device. One method ofovercoming this problem is with cross-hatched, alternating waveguides.In some cases, the device uses monochromatic illumination and detectiontechniques to avoid or mitigate such problems.

In an exemplary system, the development of low cost packaging foranalytical arrays is enabled with the use of chip scale packagingtechniques. For example, the use of through-hole vias with distributedprocessing and data collation circuitry enables the multiplexing of manyanalytical signals onto a greatly reduced number of I/O lines. Byexample, a collection of 256×256 elements each operating at 25incorporations per second and providing 5 bytes per event requires anelectrical bandwidth of about 65 mega-bits per second. This bandwidthcan be provided at only about 10% of the maximum data rate of standardLVDS signaling (ANSI-644) which only needs two connections. For a devicecapable of mapping an entire genome in 15 minutes, for example, as fewas 14 LVDS electrical connections are required as is shown in FIG. 12.

One will appreciate from the description herein that exemplaryintegrated device provides a high degree of scalability. The integrateddevices may be extended to a scalable array segment at very highresolution. In this high resolution array, the performance across thearray (periphery versus center) is made more uniform with theherein-described system architecture. One will appreciate that the sizeand arrangement of the reactor arrays and optodes is relativelyflexible. The partition of the reactor array sections and the adjacentdistribution and processing regions can be sized across a relativelywide range and each section can be spaced with respect to each other atvarying distances to support the overall function required.

Although in various respects the analytical device is described as beingfabricated in a monolithic fashion, such that all integrated elementsare fabricated from the outset into the same structure, one willappreciate from the description herein that other manufacturingtechniques may be utilized. In some cases, different components arefabricated separately, followed by integration of the separate partsinto a single integrated device structure. For example, the sensorelements, optionally including one or more optical elements, may befabricated in a discrete component part. Likewise, the reaction cellsmay be fabricated in a discrete component part optionally along with oneor more optical components. These two separate parts can then be matedtogether and coupled into a single integrated device structure where thesensor elements in the first component part are appropriately alignedwith the reaction cells in the second component part. In variousembodiments, the analytical device employs modular assembly techniques.In this manner, various components can be joined, separated, andreassembled as needed. For example, the reaction cell array andwaveguide and sensor may be assembled during an experiment and thenseparated so the cell array and waveguide can be replaced for set-up ofthe next experiment.

V. Excitation and Optical Components

FIG. 13 illustrates the general nature of optical signals from areaction cell in various aspects of the present invention. As shown, thereaction cell or region comprises a very low volume reaction region suchas a zero mode waveguide (ZMWs), e.g., ZMWs 202, disposed upon asubstrate 204. As shown in the exploded view, a ZMW comprises anunfilled core 206 or aperture disposed through a cladding layer 210 thattypically comprises a metal film layer. As described in, e.g., U.S. Pat.Nos. 6,917,726 and 7,486,865, the entire contents of which areincorporated herein for all purposes, the exemplary zero mode waveguidestructure is of sufficiently small dimensions that light that is atgreater than a cut-off frequency that enters into the waveguide core 208is not propagated through the core but exhibits evanescent decay throughthe core. This allows for efficient illumination of just the volume ofthe ZMW at the opening (schematically illustrated by the dashed linewithin core 206) and collection of any optical emissions that occurwithin the same volume. The result is to permit excitation of andcollection of fluorescent emission from individual molecules disposed atthe opening of the core, e.g., on a transparent base layer. Lightsignals from the reaction cell, or ZMW 202 as shown, are emitted in aLambertian distribution, as shown by arrows 212. Efficient capture ofsignals exhibiting this profile may necessitate either directionaloptics to re-direct the signals toward a detector or provision of adetector that matches the hemispherical surface of this signal profile.

In various embodiments, the analytical device of the invention makes useof various excitation techniques. In an exemplary embodiment shown inFIG. 14, the analytical device makes use of a top-side floodillumination method. The fluidic channels and ZMWs are opticallyshielded from topside illumination and a path to direct the light to theactive area of the ZMWs is provided. The top half of the exemplaryoptode integration socket (e.g. an ATE socket) is transparent to theflood illumination while shielding the microfluidic insert. The socketmay be made of a waveguiding material to assist with the floodillumination of the part. For example, the socket may include astructure or materials selected to guide the flood illumination along apredetermined path.

In FIG. 14, the optode array chip comprises an array of ZMWs 91 formedwithin a transparent substrate such as glass. Surrounding the ZMWs andextending into the top surface of the glass substrate are regions ofopaque cladding material comprising, for example, a metal such asaluminum or other suitable metals, a metal oxide, or a composite ofmetal and metal oxide. Illumination light 96 introduced from above thechip in flood fashion passes down through the glass and is directedupward to the bottom of the ZMWs by optical elements 95, which cancomprise mirrors or dielectric stacks. The light can stimulate emissionfrom sample within the ZMW, the emitted light from which is transmitteddown to optical detectors 97. Fluid is transported to the ZMWs by fluidconduits 92. The tops of the ZMWs are covered with an optically opaquecovering 94 which prevents the illumination light from entering the ZMWfrom above. The opaque covering 94 can comprise a metal such asaluminum.

In some aspects, the invention comprises a device for measuringanalytical reactions comprising a transparent substrate including aplurality of rows of nanoscale apertures extending through an opaquecladding to the top of the transparent substrate. The rows of nanoscaleapertures are separated by regions of the transparent substrate open toillumination from above. The device has a plurality of fluidic conduits,each on top of and in fluidic contact with a row of nanoscale apertures.For these exemplary devices, each fluidic conduit is coated with anopaque material that prevents the illumination light from entering thenanoscale aperture from above. In addition, the device has a series offeatures below the nanoscale apertures configured to direct illuminationlight from above the transparent substrate up into the nanoscaleapertures from below. In some embodiments the device also has built-inoptical detectors, with at least one detector per nanoscale aperture. Insome cases, the device has multiple detectors for each nanoscale well,for example, four detectors, each sensitive to a different color toallow for four color nucleic acid sequencing.

Various aspects of the invention are directed to waveguide architecturesexcited by laser beams that impinge on the device chip from below. Thebeams may be subjected to refractive redirection within the chip. Finalshaping may be performed with optical elements such as micromirrors(though the wavevector, k, does not change direction) and other devicesas will be appreciated from the description herein.

FIGS. 15, 16, 17, 18, and 19 illustrate various other techniques forlight-based excitation in accordance with the invention. In contrast toconventional devices making use of bottom-side illumination, theexemplary devices provide increased flexibility in the method anddirection of illumination. The increased flexibility can be important inthe exemplary case where much of the chip surface area is occluded bymicrofluidics and electronics and not available for photonic injection.

The illustrated device 430 a of FIGS. 15, 16, and 17 includes asubstrate 406 a upon which a cladding layer 405 a is deposited. Aplurality of reaction cells, in the exemplary case zero mode waveguides(ZMW) 402 a, are defined within spaces in layer 405 a. In the exemplaryembodiment, the substrate is fused silicon. Suitable materials for thecladding and ZMWs include, but are not limited to, metals and alloys,metal oxides, and composites of metals and metal oxides. In an exemplaryembodiment, the ZMWs are formed of aluminum and aluminum oxide. Anaqueous sample is positioned above layer 405 a such that particles ofinterest can move into the ZMWs.

The exemplary device utilizes modified laser-based excitationstrategies. In various respects, devices 430 b, 430 c, 430 d, 430 e, and430 f are configured similarly to device 430 a except that the devicesare illuminated with differing illumination techniques. FIG. 16illustrates illumination from different angles and directions. FIG. 17illustrates illumination with focused light and flood light.

With reference to FIG. 16, the illumination light may be directed intothe device, and in particular the reaction cells, from directions otherthan from below the device (oriented with the ZMW facing up). In variousembodiments, the illumination comes from above at an angle Φ relative tothe top surface of the device. In another instance, excitation isprovided from the side of the device. Referring to FIG. 17, theexcitation is optionally provided in flood fashion (i.e. a uniform planewave across the entire ZMW array) or as an array of two, three or morebeamlets, up to the number of active ZMWs, or even more than the numberof ZMWs. The illustrated device of FIG. 17 is configured similar to thedevice of FIG. 14 described above.

The above illumination strategies, however, may not perform well incertain sequencing systems without modification. As discussed in U.S.Pat. Nos. 7,056,661; 7,332,284; and 5,821,058, the entire contents ofwhich are incorporated herein for all purposes by this reference, takingadvantage of the photonic restriction of ZMWs generally calls for thelight to hit the respective ZMW from the bottom (substrate) side, notthe top (aqueous) side. As will be discussed below, therefore, a numberof devices and configurations may be employed to improve systemperformance with such illumination strategies.

FIG. 18 illustrates a device that optionally includes relatively largediameter light pipes that extend through the metal layer and/or otherconfigurations for allowing the light to pass through the ZMW layer tothe substrate below. In the exemplary embodiment, the metal ZMW layerincludes gaps 407 g, 407 h, and 407 i that allow light to pass throughand deflecting elements 408 g, 408 h, and 408 i for redirecting thepassing light to the underside of the sequencing layer. Alternatively,the device may include raised pedestals on the substrate with tops atvarious angles to effect the desired routing of the excitation light.Other methods for redirecting the beams/beamlets may include embeddingdevices in the metal ZMW layer or in the substrate.

The gaps or light pipes 407 may be dimensioned to correspond to theZMWs. In various embodiments, the gaps or structure for allowing thelight to pass through the top surface have a size equal to or greaterthan the size of the ZMWs, preferably twice the size of the ZMWs, andmore preferably up to ten times or more times the size of the ZMWs. Theoptional deflecting elements include, but are not limited to, metal orsemiconductor mirrors, dichroics, prisms, bragg scatterers,acousto-optic devices, and electro-optic devices. The light may bedeflected to impinge on the bottom of the ZMW at a normal incidenceangle or at another angle. Further, single light pipes may feed light toone or more ZMWs using semitransparent reflective elements.

One will appreciate that other devices and configurations may be used toallow light to pass through the sequencing layer and redirected to anunderside. In various embodiments, the device includes a waveguideassembly for receiving optical illumination and redirecting theillumination to one or more reaction cells in the sequencing layer.Referring to FIG. 19, for example, light is directed through gaps in thesequencing layer into waveguides extending below the sequencing layer.The exemplary waveguides are channel waveguides configured to funnel theillumination along a predetermined path below the sequencing layer. Thelight is optionally funneled through the waveguides to one or morerespective reaction cells from below for excitation in an otherwisesimilar manner as described above.

Referring to FIGS. 20 and 21, light is optionally collected by pillars410 k, 410 l extending upward from the substrate to a point above thesequencing layer (e.g. metal ZMW layer) 405 k, 405 l. The pillars mayhave a flat top or angled top. The top of the pillars include anillumination inlet port for receiving illumination. The exemplary tophas an angle selected based on the angle of incidence of the excitationlight so that the light is efficiently coupled into the pillar 410 l asshown in FIG. 21. The received light then undergoes total internalreflection (TIRF) such that the pillar directs the light to a channelwaveguide 414 l. The waveguide then routes the light to an underside ofone or more respective reaction cells. The optical pillars may extendabove the sequencing layer to provide a degree of shielding of thesurface. As shown, for example, in FIG. 21, the ZMWs and reaction cells402 l may be positioned in the laser “shadow” 401 l of the pillarthereby more efficiently coupling the light into the waveguides andminimizing undesirable exposure of surface-bound moieties to the laserlight. In various embodiments, the device includes an optically opaquecladding layer on top for shielding.

Referring to FIG. 22, ZMWs 402 m, 402 n and microfluidics 433 m, 433 nare optionally shielded from light from above with optically opaquewalls 470 m, 470 n. In the exemplary device, the ZMWs or clusters ofZMWs are contained in separate microfluidic channels 433 m, 433 n havingoptically opaque walls configured to block incident light and shield thechannel contents. The walls of the exemplary channels isolate the fluidand/or illumination housed therein. The shielding may be accomplishedusing various physical structures and devices. For example, the channelwall may include a thin metal coating or the device may include adielectric stack that is reflective to the light. In another examplewhere ZMWs and light pipes are in the same fluidic volume, an array ofapertures above the light pipe array may serve to minimize thenon-useful light contamination in the reagent volume.

One of skill in the art will appreciate from the description herein thatthe ZMW illumination does not need to be directed from the bottom.Illumination may also occur from other directions such as the side. Asshown in FIG. 23, an exemplary device includes a waveguide sandwichedbetween the metal sequencing layer that forms the ZMW 402 o′ and asemiconductor layer (e.g. silicon) 406 o′. The semiconductor layer mayinclude optoelectronic materials. In contrast to device 430 o, exemplarydevice 403 o′ includes a waveguide 414 o′ that receives illuminationfrom an edge (side) of device and directs the light to ZMW 402 o′. Theexcitation light may be applied to sample in the ZMW from the side orbottom via the waveguide. The exemplary device provides a compact designfor efficient illumination of a sample with increased illuminationflexibility.

Various embodiments of the invention are directed to providing a compactdevice with efficient illumination. As described above, various aspectsof the invention are directed to a compact, scalable system withreaction cells, sensing elements, and other functions integrated into aunified device.

Some of the description above relates to integrated sequencing sensorsutilizing illumination confinement to small molecular volumes. Suchtechniques require compact and efficient illumination methods to operateat high resolution for low cost sequencing. One limitation ofconventional devices is the undesirable rejection of sourceillumination. Another limitation is the difficulty of efficient routingof source illumination to the sequencing site. Both limitations may beeased with the use of through-wafer infrared illumination as discussedbelow.

Turning to FIGS. 24, 25, and 26, another exemplary device configured forefficient illumination in a compact architecture is shown. The exemplaryoptode device is configured for introducing an excitation signal frombelow the device, and in particular, the detection layer. FIG. 24 is across section of the exemplary integrated device. The device includes asubstrate 501 with patterned photodetectors 502. The substrates andphotodetectors can be a single device or an array of one, two, or moredimensions of arbitrary resolution. These photodetectors are arrangedwith conductive readout busses 503, which typically are opaque toradiation. Metal conductors are arranged in an insulating layer 504. Invarious embodiments, the insulating layer is made from an oxidedielectric and transmissive to optical radiation frequencies. Theexemplary integrated device includes a sequencing layer which is madefrom very small volume optical cavities 500 arranged over thephotodetectors 502. These volumes 500 are made from a top layer 505. Inan exemplary embodiment, the cavities 500 define reaction cells forcapturing a set of reactants. The exemplary sensor elements arepositioned essentially below corresponding reaction cells and in opticalcommunication with the reaction cells. In various embodiments, the toplayer is essentially optically opaque and biocompatible with anyrequired surface treatments to facilitate the sequencing chemistries.

In contrast to conventional devices, the exemplary device has at leastpartially overlapping illumination and detection pathways and isconfigured for receiving illumination from the bottom of the devicethrough the detection layer. As shown in FIG. 25, the exemplary deviceis configured such that the illumination is directed from below thedevice through a sensor element 502 on the way to the reaction cell 500.As shown in FIG. 26, at least some of the emitted light is directed ingenerally the opposite direction to the sensor element 502 where it isabsorbed.

The top surface of the device includes an optically opaque layer such asa cladding layer. The sequencing layer is optionally provided with atransparent substrate and a plurality of nanoscale apertures extendingtherethrough. Each aperture is separated by regions of transparentsubstrate. A layer 501 is provided below the sequencing layer. Theexemplary layer 501 includes electrical vias and fluidic conduits,generally designated 523. A detection layer is provided below layer 501.A plurality of sensor elements 502 are disposed in the detection layer.A waveguide may be optionally integrated into the device to directillumination to the reaction cells.

The exemplary device is configured for use with upconverting dyes.Generally, upconverting dyes absorb wavelengths longer than theiremission wavelength. Through multiple photon absorption, they generatehigher energy output photons. U.S. Pat. No. 7,056,661, previouslyincorporated herein, discloses an exemplary polymerase provided with adonor fluorophore that is excited at a first wavelength and emits at asecond wavelength while the nucleotide to be added is labeled with afluorophore that is excited at the second wavelength but emits at athird wavelength.

In general, the reactants include a dye or similar material thatreceives illumination of a first energy level and emits illumination ata higher second energy level in response. In various embodiments, theset of reactants delivered to the reaction cell includes an upconvertingphosphor for receiving two or more photons of a first energy level andemitting fewer photons of a second energy level in response, the secondenergy level being greater than the first energy level. In variousembodiments, the phosphor dye receives two or more photons and emits ahigher level signal in response. In various embodiments, the dyereceives one or more photons and combines the photons into a few numberof photons having a longer wavelength (higher energy level).

In operation, the illumination light 550 is directed to the reactioncell 500 along an illumination (transmission) pathway under sufficientconditions to cause the phosphor to emit a detection signal. Theexemplary transmission optical path is shown in FIG. 25. The exemplaryreturn optical path for the dye emission is shown in FIG. 26. Theemitted rays are absorbed by the upconverting dye 502′.

The exemplary device receives a dye having an emission wavelengthselected near a detection edge of the sensor. In general, the dyereceives illumination at a first energy level and emits a detectionsignal at a second, higher energy level. Whereas the sensor element istransmissive at the first energy level, the emitted detection signal isat a sufficient energy level such that it is absorbed by the sensorelement. In this manner, illumination may be directed into the devicefrom below the chip and through the sensor element. This technique alsoprovides a compact design by combining the transmission and detectioninto integrated pathways.

The exemplary device is designed, in part, based on the generalprinciple of selecting the dye wavelength near the detection edge of thephotodetector and substrate. In other words, the stimulus wavelength istransmissive to the detector layers while the emitted wavelengths areabsorbed by the detector layer. This can be accomplished by adjusting atleast one of the illumination wavelength, detector, and dye based on theothers. One will appreciate that this provides a method toadvantageously illuminate the sequencing layers through the detectorlayer and utilize an identical (but opposite direction) path foremission and detection. By utilizing a common path, a simpler device canbe produced at lower cost and decreased space requirements (e.g.vertical profile).

FIGS. 25 and 26 illustrate various other components for routingillumination in the exemplary device. In various embodiments, focusingelements aligned during manufacture are used to increase efficiency. InFIG. 26, an optional microlens 501′ is patterned on the back surface ofa wafer 501 and directs light rays 550 towards the sequencing layer 500.

As will be appreciated from the description herein, the above techniquecan also be used to route illumination away from the opaque conductinglayers and other components, for example, to increase efficiency orintroduce light scattering sites. As shown in FIG. 25, for example, afocusing element directs the illumination through the sensor elementinto the reaction cell and away from the cladding material. In variousembodiments, the focusing element is patterned in the conducting layerwith index gradients (e.g. nitride or air gap) or using metal or otherreflective guiding devices. In various embodiments, back surfaceillumination is achieved with hybrid assemblies and/or techniquesdescribed herein. For example, back surface illumination may be achievedwith self-aligned optical assemblies described above.

With reference to FIG. 27, one will appreciate that the above techniquescan be used with a downconverting tail technique, in which the longerwavelength tail of the dye absorption is used with the short wavelengthtail of the emission distribution to enable detector layer filtering.

Various other optical components may also be provided on or integratedinto the analytical device for routing and adjusting the illuminationsignal. FIG. 28 illustrates an exemplary device 630 that makes use oftotal internal reflection (TIRF) techniques. Conventional TIRF methodsgenerally require either a prism for coupling high-angle radiation to asubstrate or through-the-lens coupling of marginal rays above thecritical angle of total internal reflection. Both conventional methodsmay have drawbacks. For prism TIRF, much of the emitted radiation islost because the emission is biased in a direction away from theobjective lens. In through-the-lens TIRF, high angles are not generallyachievable in high index materials. Therefore, a method of doingthrough-the-lens TIRF with high angles of incidence as described hereinis thus desirable.

In the exemplary device of FIG. 28, a substrate 605 is modified withnotches 601 with angled sidewalls 603 to redirect light that is incidentnear the zero angle to very high angles of incidence, irrespective ofthe index of the substrate. In various embodiments, the angle ofincidence is below the critical angle for TIRF and the notches redirectthe light at an angle above the critical angle. In various embodiments,the angle of incidence is below the critical angle for directlyilluminating the sample and the notches redirect the light at asufficient angle for illumination.

The notches need only be wide enough to allow the beam to be directedtoward the region of interest while allowing sufficient opticalresolution of the ROI from region 606 (also referred to “bank-shotregion”). The quality of the surface generally must be sufficient to getan appreciable amount of energy at large incident angles. Althoughdescribed as notches, one will appreciate that other guiding mechanismsmay be used in accordance with the invention.

FIG. 29 illustrates other optical components for adjusting,manipulating, and controlling the direction of the excitation light inaccordance with various aspects of the invention. The exemplary devicesare made using a variety of techniques which include grinding thematerial with v-shaped cutting edges, photolithography with variabledepth pattern transfer, wet etching with undercut, and other methods. Inanother embodiment of the invention, a notch in a transparent substrateis formed by polishing the edge of a flat plate of glass at an angle,then affixing two such slides to a reservoir so that the acute anglesformed at the edge are in close proximity or in contact. An hermeticseal is then achieved by placing a small quantity of curable sealant inthe cleft formed between the two plates, which will then form a seal bycapillary action across the entire length of the joint. One willappreciate that other modifications will be within the scope of theinvention. For example, the angle of the bank shot surface, the width,the presence or absence of a partner surface, and other modificationsmay be made.

In another aspect of the invention shown in FIG. 29, an exemplary deviceis formed of a high index of refraction base substrate. In operation,illumination light is directed into the substrate to cause dark-fieldillumination or total internal reflection illumination (TIRF) of the topsurface. The top surface includes zero mode waveguides (ZMWs) fabricatedfrom a lower index of refraction material. The illumination creates thesame observation volume confinement created in regular ZMWs, but thetransparent nature of the top surface layer reduces scattering of theincident light. Suitable materials for the substrate include, but arenot limited to, lithium niobate, zirconia, diamond, and other high indexmediums capable of being machined.

In the exemplary device, wedges with angled sidewalls are ground intothe substrate to promote total internal reflection (TIRF). The wedgesare machined in the substrate and include conical features on thesurface configured to generate a focusing effect around the zone inwhich TIRF is to be created. This allows more efficient use of theincident radiation. This may also reduce background light fromauto-fluorescence and stray laser light. These conical features andwedges can be fabricated by surface micromachining, thin filmevaporation, and the like.

In various embodiments, a small light-blocking element is included withthe device for blocking direct light path to the zone of detection andpreventing light from being refracted into the liquid medium containingthe analyte, thus reducing background radiation. In various embodiments,the light reflecting surfaces are slightly concave (i.e. deviating froma true conical shape) thereby allowing additional focusing so a singlepoint can be either transmitted directly to a detection system orreflected off the conical or nearly conical surfaces to be directedtowards the detector. In this way the numerical aperture of collectionmay be greatly increased. This may have importance in fluorescenceemission systems near high index media due to the directionalnonuniformity of emission.

As will be appreciated from the description herein, because the devicesof the invention are generally amenable to fabrication using standardmonolithic semiconductor fabrication techniques, fabrication of thedevices can also incorporate many of the functional components that areemployed for the illumination and detection elements, e.g., theelectrical interconnects and busses used for a CMOS sensor array as wellas the optical components (e.g. optical tunnels, lenses, mirrors, etc.)and even the reaction cells themselves (e.g., metal clad ZMWs). Inaddition, other functional elements may be integrated using the same orsimilar processes, including, for example, microfluidic elements thatmay be integrated into the overall device structure, and illuminationcomponents such as for delivery of excitation illumination to thereaction cells.

As referred to above, in some cases, illumination optics are includedwithin the integrated device structure. These optics may include actualillumination sources, e.g., LEDs, solid state laser components, or thelike. They may also include optical conduits for transmission ofexcitation illumination from either an internal or external light sourceto the reaction cell. Examples of optical conduits include waveguidesintegrated into the substrate adjacent to the reaction cell. Examples ofsuch illumination conduits have been previously described in, e.g.,published U.S. Patent Application No. 2008-0128627, the full disclosureof which is incorporated herein by reference in its entirety for allpurposes.

Similar fabrication processes may be employed to provide higher index ofrefraction (IR) material tunnels from the reaction cell to the sensorelement, or devices that include a hybrid of a high IR tunnel componentand a reflective (e.g. metal) optical tunnel. In an exemplaryembodiment, one or more intermediate layers are provided with regions ofhigher index of refraction. These regions are of sufficiently high IRrelative to the surrounding substrate material so that they funnel lightto the detector and/or reaction cell by virtue of maintaining totalinternal reflection within the higher IR region. By way of example, ifthe high IR region possesses an IR of e.g., 2.04, such as is the casefor a silicon nitride plug, that is disposed through and interfaced withan intermediate layer having an IR of 1.64, e.g., as in silicon dioxide,it would result in total internal reflection of any light impinging thatinterface at less than 30 degrees. As will be apparent from thedescription herein, a variety of methods are available for providinghigh IR regions precisely located within the substrate layer and otherlayers may be used including, but not limited to, etching followed bynitride deposition (e.g., liquid phase chemical vapor deposition(LPCVD)). Other index shifting materials may be included in thefabrication of the device, including, for example, doped silicamaterials, e.g., nanocrystal doped components or materials (e.g., U.S.Patent Application No. 2007-0034833, the full disclosure of which isincorporated herein by reference in its entirety for all purposes),and/or air or other gas-filled gaps or spaces to provide index mismatchto guide optical signals. In various embodiments, the device includesoptical tunnels with confined cavities. The optical cavities may beuseful in a variety of ways depending upon the nature of the applicationand architecture of the device. For example, such cavities may provideadditional signal funneling to a detector or sensor element.Alternatively, the cavities may be configured as an illumination conduitfor delivery of illumination radiation to a reaction cell.

In various embodiments, the illumination source is remote and directedinto the device with various optics. In various embodiments, theillumination source is reversibly optically coupled to the illuminationports. By “reversibly optically coupled” it is meant that one element,which is functionally coupled to another element, may be removed. Inother words, the coupling is not permanent. As used herein, for example,the illumination source may be connected and disconnected from theillumination port using quick disconnect ports and the like.

VI. Detector Components

As noted previously, in some applications, it may be desirable todistinguish different signal components, e.g., to identify that both areaction has occurred and to identify the participants in that reaction.By way of example, in the case of nucleic acid sequencing, one canprovide different nucleotides with different optical labeling groupsthereby allowing not only detection of a polymerization reaction butalso identifying the particular type of nucleotide that was incorporatedin that polymerization reaction. Accordingly, it would be desirable toinclude the ability to distinguish different signal components withinthe devices and/or systems of the invention.

In some optical systems, the ability to distinguish different signalcomponents is achieved through the use of, e.g., different filteredoptical trains, or the inclusion of dispersive optical elements todifferentially direct different spectral components of a signal todifferent detectors or different regions on a given detector array. Invarious embodiments, the system is configured for detection anddifferentiation based on other detection techniques. Various aspects ofthe detection devices and methods are similar to those described in U.S.Patent Publication Nos. 2007/0036511 filed Aug. 11, 2005, 2007/0036511filed Aug. 11, 2005, 2008/0080059 filed Sep. 27, 2007, 2008/0128627filed Aug. 31, 2007, 2008/0283772 filed May 9, 2008, 2008/0277595 filedSep. 14, 2007, and 2010/0065726 filed Sep. 15, 2009, and U.S. Pat. Nos.7,626,704, 7,692,783, 7,715,001, and 7,630,073, the entire content ofwhich applications and patents are incorporated herein for all purposesby this reference.

In the context of integrated devices, the available space for use indifferential direction of signal components is generally reduced.Similarly, where a single sensor element is assigned to a reaction cell,one may be unable to direct different components to different detectors.

The integrated device may include directional components and/or filtercomponents that selectively direct different spectral components of asignal to different adjacent pixels or sensors within the device. By wayof example, a given reaction cell and its associated optical train mayinclude multiple individual sensor elements associated with it, e.g.,pixels. Included within the optical train would be a directionalcomponent that would direct spectrally distinguishable signal componentsto different sensor elements or collections of sensor elements. Examplesof such components include prisms, gratings or other dispersive elementsthat can redirect and separate signal components. The use of suchcomponents in optical systems is described in, e.g., published U.S.Patent Application No. 2008-0226307, the full disclosure of which isincorporated herein by reference in its entirety for all purposes.

As noted previously, although generally illustrated in terms ofindividual or a few reaction cells and associated integrated opticalcomponents and sensors, it will be appreciated that the illustrationsand descriptions provided herein apply to much larger arrays of suchreaction cells. In particular, such devices may generally haveintegrated into a single device more than about 1000 discrete reactioncells, and associated optics and sensors. In various embodiments, theintegrated device includes a number of reaction cells in a rangeselected from between about 1000 and about 1 million, between about 2000and about 1 million, between about 1000 and about 100,000, between about100,000 and about 1 million, between about 1 million and about 10million, and more than 10 million. It may be desirable to select thenumber of reaction cells based on the desired application. For example,the device may include between about 1000 and about 100,000 cells forclinical testing, between about 100,000 and about 1,000,000 for adiagnostic laboratory, or more than about 1,000,000 for high throughputresearch.

In accordance with the invention, each reaction cell may have anindividual sensor element or pixel associated with it, or it may havemultiple sensor elements or pixels associated with it (particularlywhere spectral separation, direction and separate detection arewarranted). Likewise, each reaction cell may preferably have its owndedicated integrated optical components associated with it. In somecases, integrated optical components may be shared among multiplereaction cells, e.g., to apply standard filtering, to apply illuminationto multiple cells, or the like, and will typically be in addition to oneor more dedicated optical components.

In accordance with the present invention, in addition to integration ofthe sensor and reaction cell elements within a single analytical device,one or more optical components may be included within the device.Examples of integrated optical elements include, but are not limited to,directional optical elements, i.e., optical elements that alter thedirection of optical signals to direct those signals at or to a sensorelement or another optical element. Such elements include, e.g.,mirrors, prisms, gratings, lenses, and the like. By way of example, incertain cases, parabolic reflector elements or micro-mirrors areintegrated into the device to more efficiently direct optical signals ina given direction (See, e.g., U.S. patent application Ser. No.12/567,526, filed Sep. 25, 2009, incorporated herein by reference in itsentirety for all purposes). Other optical elements include spectralelements, e.g., elements that alter the spectral characteristics of theoptical signals including directing spectral components of a signal orset of signals in differing directions, separating a signal intodifferent spectral components, or the like. These elements include, forexample, dichroics, filters, gratings or prisms that separate a givensignal into spectral constituents.

In various embodiments, such optical components include containedoptical enclosures that efficiently collect photon signals emanatingfrom the reaction region and that are incident over a wide emissionangular distribution, and direction of those signals to an assignedsensor element or elements. Such self-contained enclosures typicallyprovide trapping within the chamber of substantial amounts of thephotons emitted from the reaction region, elimination of cross talkbetween reaction cells or regions that would otherwise result fromscattered signal entering adjacent sensor elements, reduction in leakagecurrent since the sensing elements can be made extremely small, reducingscattering paths and scattering elements within each optical chamber,and reducing auto-fluorescence due to the substantially reduced opticalpath mass and eliminated free-space interfaces.

In addition to such directional optical elements, or as an alternativeto such elements, multiple sensor elements may be provided withfiltering optics that allow only a single signal type to reach thatparticular sensor element. Each sensor is differently filtered to allowit to detect a particular signal component, to permit multicolordistinction. In particular, each of a plurality of sensor elementswithin a given reaction cell's dedicated optical train is provided witha filter that narrowly passes one component of the overall signal fromthe reaction cell. For example, the signal associated with a givennucleotide incorporation event would be passed by a filter on a firstpixel element, but rejected by the filter on three other adjacent pixelelements. Each of the different filter layers on each sensor would beselected for the given signal components for a given application.Further, each reaction cell could have one, two, three, four, or morepixel elements dedicated to receiving the signals from that reactioncell. In some cases, 5, 10, 20, 50 or even 100 pixels or more could bedevoted to a given reaction cell.

Deposition of a variable filter layer, i.e., providing different filterson different pixels or collections of pixels, may generally beaccomplished during the fabrication process for the overall integrateddevices or the underlying sensor elements using conventional CMOSfabrication processes. Likewise, dichroic filters are equally amenableto fabrication/patterning onto the sensor elements to reject anypotential excitation illumination.

Alternatively, or in addition to selective direction/filtering of theoutput signals from a reaction cell, distinguishing signal componentsmay also be accomplished by detecting an output signal in response to aspecific excitation event. In particular, if a signal is received inresponse to an excitation radiation that is specific for a given signalgenerator, e.g., fluorescent label, one can assume that the label ispresent. By modulating or interleaving the excitation illuminationacross the excitation spectra for multiple fluorophores having differingexcitation spectra (or different excitation/emission profiles), one canidentify when any of a set of fluorophores is present in the reactioncell. By correlating an emitted signal with a given excitation event,one can identify the fluorophore emitting the signal. Examples of thisprocess are described in published U.S. Patent Publication No.2009/0181396, the full disclosure of which is incorporated herein byreference in its entirety for all purposes. As will be appreciated, thetiming of illumination, the frame rate of the detector, and the decaytimes for the fluorophores may be matched to provide optimaldetectability of each different signal event, without different eventsbleeding over into each other, while also permitting sufficient samplingduring a given frame capture event for the detector so individual eventsare not missed.

In an exemplary process, a given application that includes multipledifferent labeled species, e.g., different labeled nucleotides, includeslabels that differ in their excitation spectra. Illuminating a reactionmixture iteratively with the different wavelength excitation sourcesprovides temporal separation between excitation of the different labels.By correlating an emitted signal with one of the different excitationwavelengths, one can interpret the signal as emanating from a givenlabel. In operation, one can cycle through the various differentexcitation sources at high frequencies, and detect the correlatedemissions at equivalently high frequencies. This is illustrated in FIGS.30A, 30B, and 30C. As shown in FIG. 30A, different excitation sourcesare pulsed in an interleaved fashion. Exemplary timescales of suchpulses are illustrated in FIG. 30B, along with the correspondingexpected residence times of detectable species, and the expected signalsthat would emanate from those species. Also shown is the pixelintegration over a given frame that includes multiple cycles through thevarious excitation pulses.

FIG. 30C shows simulated integration and detection of a signal from alabeled reactant (left half of plot), and the absence of a labeledreactant (right half of plot), even in the presence of high noise levels(pulse extraction with a signal of 0.5 electron/sample and 6 samples perframe and a 1 electron background).

In accordance with the invention, an integrated smart pixel can beemployed in efficient detection and distinction of the various signalelements that would derive from the foregoing. A schematic of the pixeldesign is provided in FIG. 31. As shown, the pixel including aphotodiode 1102 includes four integrated storage elements 1104, each ofwhich may be electronically gated by the activation of a separateexcitation source. In such cases, a modulated controller element wouldbe coupled to both the detector and the excitation illumination sourcesto synchronize the illumination and storage events. As a result, eachstorage element will be correlated to a given excitation event andconsequent emission event, such that detected signals for each differenttype of excitation event are relegated to a different storage element.

In addition to being correlated to discrete excitation events,additional correlations may be pre-programmed into such systems. Forexample, any delay between an excitation event and an emission profile,e.g., for a given type of labeling group, may be preprogrammed into thepixel so as to take such delays into account in the detection event.Likewise, all storage elements could be switched off during intermediatestages of the excitation process, to avoid any noise contributions,slower decay rates of some signals, etc. As shown, and as will beappreciated, conventional logic elements, amplifiers, etc. are alsoincluded.

The exemplary pixel detector of FIG. 31 contains steering logic andmultiple integrating nodes. The nodes can be run simultaneously orswitched during optical integration periods. The photodiode 1102 isconnected to a plurality of integrating and processing nodes 1104. Thesenodes are generally connected to the photodetector via transfer gates(TXn). In depletion mode, these channels are non-conducting (i.e. open)when a low voltage is applied to the gates. When a high voltage (e.g.several kT above the transistor threshold voltage) is applied, however,a conducting path is made between the nodes and the photodetector. Invarious embodiments, each integrating node is independently reset toclear the previous charge from its circuits prior to transferoperations. Although the exemplary photodetector uses CMOS, NMOS or PMOStechnology, any MISFET, BJT or other switching circuit elements can besubstituted without altering the basic disclosed operation.

The use of multiple integrating nodes on a common photodetector can beused to separate photocharge events of many causes. In variousembodiments, the detector is configured as a vertical detector wherebythe depth of absorption of photons in the detector is related to itsenergy level. Having multiple collection nodes at different depths inthe detector provides a method to determine the color of the incidentillumination by comparing the relative strengths and absorption depth ofthe signals. In this case, generally all the transfer gates are activesimultaneously and the optical integration time can be controlled by thetransfer gate active duration time. Based on the previous events, eachintegration time can be different to essentially equalize or extend theoperating dynamic range.

In various embodiments, the arrival time or resonant phase of a photonto a regular or synchronized event can be used to classify the speciesof the signal. If each signal is responsive to different input stimulus,the stimulus can be applied in a regular and sequential fashion. Bysynchronizing the stimulus with an unique integrating node, the speciescan be determined. If a lag in response to a frequency modulation of thestimulus (chirped, swept, constant) exists, this phase margin can bedetected by appropriately delaying the transfer gate to each integratingnode with the in-phase signal from the stimulus. In each of these cases,the relative response from each integrating node can be used topositively identify and classify the species.

One will appreciate that this architecture can also be used to determinehigh speed events (sub-frame rate) by storing multiple sub-frame samplesthat could have temporal overlap. In various embodiments, the detectorincludes local storage within pixels to achieve high speed burstcollection.

VII. Overall Analytical System Architecture

A large number of optical analyses, including those described herein,utilize a common overall analysis system architecture. In variousembodiments, the present invention is directed to a scalable systemarchitecture utilizing a plurality of analytical assemblies (optodes).The exemplary system further includes a sample delivery assembly and aprocessing system.

In various embodiments, the analytical device is an integrated, portabledevice configured for local data stream processing. In one example, asingle-use analytical system includes 60,000 individual analyticaldevice elements grouped in an area less than about 1 mm². Sample can beprepared off the device and introduced into the device via microfluidicschannels, e.g., fluid delivery system 33 In various embodiments, theanalytical array includes local, integrated components including, butnot limited to at least one of a fluidics system, a power source, anillumination system, a detector, a processing circuit, a controller,steering logic, and electrical connections. The exemplary deviceincludes a portable, on-chip, battery-powered light source (i.e. LED orlaser) and a single FPGA can process the data stream (e.g. 65,000samples at an average of 25 bases per second). The detection methodsdescribed herein can be adjusted to maintain a bandwidth where a singleLVDS channel would interface to the FPGA and a standard PC interface canbe provided from the FPGA output to the external analysis equipment.

Although the analytical devices of the present invention typicallyinclude multiple elements for an analytical system integrated into asingle device architecture, it will be appreciated that in many cases,the integrated analytical devices may still employ a companioninstrument system to provide additional functionality for the analysisof interest. In particular, as noted previously, in some cases theillumination of optical analyses will utilize an illumination sourcethat is separate from the integrated device structure. For example,lasers, LEDs or other conventionally employed illumination sources maybe provided within a larger instrument that is mated with the integrateddevice. Likewise, power supplies for the integrated device, whereneeded, may also be provided within an instrument architecture. Inaddition, any environmental controls, fluidics, fluidic controlcomponents (whether electrokinetic, pressure based, or control ofintegrated pumping and valving mechanisms, or other) may be providedwithin the instrument architecture. As will be appreciated from thedescription herein, any number of these components may be integratedinto the system or connected remotely. For example, the illuminationcomponents can be integrated into the system with a system platform andconnected to the analytical device array with a test socket as describedabove. In another example, the illumination components are provided in aseparate illumination instrument and connected to the system inconventional manner.

Where such other functionalities are provided within an instrumentarchitecture, such an architecture may include one or more interfacesfor delivering the particular functionality to the integrated device.For example, optical interfaces may include fiber optic connections,optical trains or other optical interfaces to provide illumination tocomplementary connections on the integrated device, which thencommunicate that illumination to the reaction cells or otherwise, asnecessary.

Electrical and data connections may also provide the requisite power anddata communication between the sensor components of the device and aprocessor that may be integrated into the instrument architecture, orthat may be exported or communicated to an associated computer that isexternal to the instrument itself.

Fluidic interfaces are also optionally provided within the systemarchitecture for easy delivery of reaction components to the reactioncells. In various embodiments, the fluidic interface comprises fluidconnectors that permit the sealed connection of fluid reservoirs in aninstrument with complementary connections on the analytical device,including, for example, fluidic manifolds with controllable valving andpumping mechanisms. In various embodiments, the fluid connectors areprovided on a test socket into which the analytical device array isseated.

Other interfaces include, for example, control interfaces with thedevice for controlling movement of fluids around an integrated device.Such interfaces may include electrical interfaces, e.g., to driveelectrokinetic transport or to power integrated pumping and valvingmechanisms, or pneumatic or hydraulic interfaces, to perform similarcontrols.

One of skill will appreciate from the description herein that the systemand method of the present invention generally increases flexibility,promotes scalability, and reduces costs. The system architecture of theinvention enables many concurrent sequencing applications. By developingsystems with common design elements, great economy of scale may beachieved and result in overall reductions in part costs, field serviceand development time and resources. Bundling parts across theseapplications may provide enhanced buying power and better ability tomanage yield and overall quality.

One will appreciate from the description herein that any of the elementsdescribed above can be modified and/or used with any of the otherelements, in any combination, in the system in accordance with thepresent invention.

VIII. Other Excitation Techniques

Various aspects of the invention are directed to a system whereby thereactants in the waveguides are excited by means other than directimpingement with a laser and the like. Turning to FIGS. 32-41, a systemincluding devices for illumination with surface plasmons will now bedescribed. There is increasing interest in the use of plasmons to excitefluorophores and other materials at least because the use of plasmonsmay have advantages in imaging small volumes like zero mode waveguides.

Conventional techniques for creating plasmons and using plasmons on asmall scale (e.g. to excite fluorophores) are described in RadiativeDecay Engineering Surface Plasmon Coupled Directional Emission,Analytical Biochemistry 324 (2004), pages 153-169; UnidirectionalUltracompact Optical Nanoantennas, Nano Letters, 2009 Vol 9 #62343-2349; Focusing Surface Plasmons with a Plasmonic Lens, Nano Letters2005 Vol 5 #9 1726-1729; Plasmonic Lens Made from Multiple ConcentricMetallic Rings under Radially Polarized Illumination, Nano Letters 2009Vol 9 #12 4320-4325; and Squeezing Visible Light Waves Into A 3 Nm ThickAnd 55 Nm Long Plasmon Cavity, Physics Rev. Letters 2006 #96 097401-1.

Plasmons are quanta of vibrational energy formed when radiation isincident on a metal surface. The term “surface plasmon polariton” (SPP)is used to describe optically-induced electron oscillations. Waveguidescan be fabricated to utilize resonant plasmonic energy with relativelylong coherence to transmit optical energy or information over adistance. See Nanohole Chains for Directional and Localized PlasmonExcitation, Nano Letters 2010, 10 285-290; A Plasmonic Dimple Lens forNanoscale Focusing of Light, Nano Letters 2009 V9 NIO 3447-3452.Alternatively, plasmonic antennas can be used to enhance the detectionand emission of plasmons at wavelengths below the photonic stimulationradiation wavelength to enhance operation of zero mode waveguides invery small volume interrogation. See Unidirectional Ultracompact OpticalNanoantennas, Nano Letters 2009 9 6 2343-2349; Manipulating NanoscaleLight Yields with the Asymmetric Bowtie Nano-colorsorter, Nano Letters2009 9 12 4505-4509. Direct coupling of light waves into sub-wavelengthapertures can create SPPs with high efficiency (e.g. up to 28%). SeeCoupling Efficiency Of Light To Surface Plasmon Polariton For SingleSubwavelength Holes In A Gold Film, Optics Express 2008, 16, 5, 3420.

The exemplary analytical devices and zero mode waveguides making use ofSPP techniques yield several advantages. By directing optical energy toan area proximal to the zero mode waveguide where a plasmonic generatoris located, excitation of fluorophores located near the source may beenhanced. The Plasmonic resonators of the invention may also be used tolocalize energy to a smaller volume than that performed by theevanescent decay of photonic electromagnetic (EM) waves. By shieldingthe optical signal path from incident photonic energy, one may eliminatethe need for optical source filtering and the broader bandauto-fluorescent background signal that is generally associated as abyproduct of the source brightness. Because the strength of plasmonsdecreases significantly in proportion to distance, SPP techniques mayalso reduce background noise in comparison to photonic illuminationtechniques.

One approach to exciting the fluorophore is shown in FIG. 32. A spot oflight is directed towards the ZMW and limited by diffraction limits atthe incident light wavelength.

$d = \frac{\lambda}{2{n \cdot \sin}\; (\alpha)}$

This approach may have drawbacks, however. The diameter of the exemplaryZMW is much smaller than the diameter of the first minimum of the Airydisk from the spot illuminant. In addition, the absorption of photonicenergy by a fluorophore dye is limited to a cross-section approximatelyequivalent to the dipole length (approximately 1 mm). Therefore, thearea ratio between the incident spot size and the fluorophore dipole isover 2 million to one. Additionally, evanescent decay of the incidentlight into the ZMW further reduces energy transfer efficiency.

To overcome the efficiency loss, very high illumination levels are usedto excite the fluorophore. This may require significant filtering of thereflected incident light from the camera, and the high intensity causessignificant auto-fluorescence in the optical components must be furtherreduced.

An alternative approach is to confine the optical energy to a smallerspot located at the dipole of the illuminant. As demonstrated in theequation below, an incident photon wave can be approximated from theMaxwell's equations by considering only the high frequency response(assuming the magnetic response induced currents are not appreciable).

${- {\nabla^{2}E}} = {\frac{n^{2}\omega^{2}}{c^{2}}E}$

where the field is represented by a set of plane waves (x,y,z).

$k_{i} = \frac{2\pi \; n}{\lambda_{o}}$

shows that the vector is constrained by the index of refraction in theoptical materials and limits the traditional spot size to approximately(1.22*λ)/NA.

Surface plasmons may provide a method to achieve higher effectiveindices to create modes at optical frequencies with indexes that areorders of magnitude higher than for optical materials. The plasmonfrequency is determined by the relative dispersion of the wave vector atthe metal-dielectric interface. Metals have a large dispersion comparedto the relatively constant permittivity in the dielectric. Using theDrude model:

$ɛ_{m} = {1 - \frac{\omega_{p}^{2}}{\omega^{2}}}$

where ω_(p) is the plasma frequency.

Thus, it is shown that the increase in dispersion happens at higher wavevectors than from the optical field alone. Free space optical fieldsgenerally cannot generate plasmons without added momentum.

Surface plasmon modes generally tend to be quite lossy and most of theloss is in the absorption in the metal. Plasmon decay lengths aretypically less than 10 micrometers but can be enhanced by directing themajority of the energy into the dielectric layer of a device (e.g. ametal-insulator-metal device with 100s of micrometer). The QualityFactor of an exemplary metal-insulator-metal (MIM) device is generallyproportional to the metal used and the input frequency (generally about2 eV-about 3 eV).

A simplified MIM structure is shown in FIG. 33. The exemplary MIMstructure is developed with plasmonic confinement at optical frequenciesusing standard commercial foundry design rules. For example, the designrule for gate oxide thickness at the 65 nm design node is about 1.1micrometer. Oxide thicknesses greater than this can be used to tune thesystem to the plasmon wavelength required (as shown in FIG. 38). Atradeoff in propagation length and plasmon energy is made with thedielectric thickness, but with the small dimensions of the ZMW, even1-micrometer-thick-slabs producing less than about 10 nm wavelengthshave propagation constants in excess of about 400 nm.

Light with a sufficient and correct incident angle and polarization isgenerally required to generate efficient SPPs and limit skin depthabsorption. With an angle of less than 30% for aluminum, for example,greater than about 40% coupling efficiency may be possible. Thus, thisform of directed energy can form a focus to the scale of the dipole withquanta energy equivalent to the incident photons and with much higherefficiency than the 2,000,000:1 efficiency through direct spot beamillumination.

By carefully tuning the plasmonic structures to the zero mode waveguidedimensions and the incident illumination, the energy transfer efficiencymay also be optimized. One will appreciate that the wavelength of theSPP can be tuned based on the waveguide dimensions and the incidentoptical illumination wavelength. This decouples the ZMW dimensions fromthe optical excitation wavelength to allow for greater designflexibility. One will further appreciate, therefore, that the ZMW can betuned to maximize performance to the chemical kinetics and emitted lightprofile requirements. Conventional photonic illumination techniquesrequire sizing the ZMW based on the photonic wavelength. For example, aZMW with a diameter much less than 100 nano-inches could be used toincrease SPP absorption by the fluorophore as well as increase thedensity of and array of ZMW elements.

In various embodiments, the method in accordance with the presentinvention includes illuminating the fluorophore in a ZMW well withplasmons. In various embodiments, the plasmons are generated within apropagation length (e.g. about 500 nm) from a photonic source that isshielded from the detector optical path. The device of the inventionalso inherently insulates the excitation with SPPs from the incidentphotonic signal in the waveguide thus reducing noise.

FIG. 34 shows an exemplary system for illuminating a reactant in areaction cell using SPPs. The exemplary system, generally designated 700a, includes a planar waveguide 710 a for receiving light from a lightsource and one or more apertures within the planar waveguide. Theexemplary waveguide is configured as a funnel with a narrow conduitportion having a diameter of about 5 nm. The planar waveguide isdisposed within a metal enclosure for generating SPPs in response tooptical energy from the waveguide.

The apertures are formed to define reaction cells 702 a for housing aset of reactants. In an exemplary embodiment, the reactants include oneor more reactants labeled with a fluorophore 704 a. In general, theplasmonic energy may be absorbed by a fluorophore, quantum dot, or anyother tag material to signal the presence of a reagent molecule. Thissignaling material may emit an energy that is distinct from the incidentplasmonic field.

Turning to FIGS. 35-41, an exemplary device 700 with a layered structureand a plurality of reaction cells is shown. The exemplary deviceincludes a metal layer 712 configured to generate SPPs based on plasmonmodes in response to optical energy. A dielectric slab 714 extendsbetween top and bottom portions of the metal layer. Waveguide 710 isdisposed between the metal layer and dielectric slab. The waveguide isconfigured to receive optical energy and transmit the optical energy tothe metal layer similar to the waveguides discussed above. The devicefurther includes reaction cell 702 disposed between adjacent ends of thedielectric slab 714 and metal layer 712.

The exemplary device is generally separated into various regionsconfigured for adjusting the introduced light, generating SPPs inresponse to the light, and applying the SPPs to the reaction cell.Moving from the center of the device outward, the device includes afirst region having reaction cell 702 configured to receive afluorophore and/or other reactants. A second region laterally adjacentthe first region includes a metal-insulator-metal (MIM) structure forproviding plasmonic energy to the reaction cell. The MIM structure isformed of slab 714 sandwiched between metal layer 712. Waveguide 710includes a thin conduit portion 710 a extending between a portion of atop surface of slab 714 and a bottom surface of metal 712. A thirdregion includes a MIM structure and a waveguide transition portion 710b. The waveguide transition portion is dimensioned and configured forfunneling optical light to the MIM structure. A fourth region extendsalong an outer portion of the device and includes an optical waveguideinlet 711 for receiving and introducing optical energy into thewaveguide. The exemplary inlet is positioned along a side edge of thedevice.

In the exemplary device, the waveguide is a planar waveguide, and inparticular a tapered lateral illumination conduit aligned with thereaction cell. The illumination conduit comprises a circular taperforming a disk of plasmonic energy. As shown in FIG. 40, in variousembodiments the system includes MIM layers with a plurality of aperturesextending therethrough to define reaction cells. In various embodiments,the MIM structure and waveguide are essentially concentric rings and thereaction cell is positioned in a center of the ring. The waveguideextends around at least a portion of a circumference of the reactioncell. Although the exemplary waveguide extends entirely around thereaction cell, one will appreciate that that the waveguide can extendaround only a portion of the reaction cell. For example, the waveguidestructure may be configured as an antenna or projection with thereaction cell positioned at one end.

Referring to FIGS. 35, 37, and 39, exemplary transition portion 710 b istapered with a decreasing thickness. The transition includes a smoothand linear shape to funnel the optical energy into the conduit 710 a andMIM with minimal losses. A dimension and shape of the taper may beselected to achieve a desired resulting plasmonic wavelength in themetal layer based on a wavelength of the introduced optical energy aswill be appreciated by one of skill in the art from the descriptionherein. The exemplary transition portion is dimensioned and configuredto decrease dispersion of the photonic wave vector at themetal-dielectric interface. In an exemplary embodiment, the waveguidetaper 710 b is fabricated with a single angled surface to be morecompatible with standard semiconductor processes as shown in FIG. 36.

The exemplary dielectric slab 714 is an electrical insulator configuredfor plasmonic confinement of the waveguide 710. The dielectric slab mayextend along all or only a portion of the waveguide. The deviceoptionally includes a cladding layer 716 in the fourth region forisolating the waveguide from the metal layer and confining opticalenergy in the waveguide. The cladding layer extends along the waveguideinlet toward to the transition portion. A top portion of the waveguidetransition portion is open to the metal layer such that as the opticalenergy moves into the transition portion some of the energy istransferred to the metal layer to cause the metal to resonate andgenerate SPPs.

One will appreciate from the description herein that the interfacebetween the waveguide and metal layer may be modified depending on theapplication and desired result. The waveguide may be physicallyseparated from the metal layer with shielding and the like. As shown inFIG. 33, for example, the optical wave may be confined within a portionof the MIM structure by a high refractive index boundary. One willappreciate that other structures and configurations may be used toconfine and direct the optical energy and plasmons in the device.

Referring to FIGS. 39, 40, and 41, the device includes a sensor element720 disposed in a substrate 721 below slab 714 and metal layer 712. Thesensor element is in optical communication with the reaction cell alonga detection pathway as shown in FIG. 41. In the illustrated embodiment,the sensor element is positioned essentially below the reaction cell andan optical tunnel is provided to focus an emitted signal from thereaction cell to the sensor element.

As noted above, the use of SPPs for excitation allows for shielding thereaction cell and detection pathway from optical energy. In variousembodiments, the device includes an optically opaque top layer forshielding the reaction cell and the detection pathway.

In various embodiments, the introduced optical energy is light having awavelength of about 0.5 micrometer. In various embodiments, the lighthas a wavelength of about 650 nm, and preferably about 647 nm. In anexemplary embodiment, reaction cell 702 has a diameter of less than orequal to about 0.6 micrometer. In various embodiments, the reaction cellhas a diameter of less than 200 nm, and preferably about 180 nm, andmore preferably about 50 nm. In an exemplary embodiment, waveguide 710has a thickness of about 1 micrometer in a region adjacent the reactioncell. In an exemplary embodiment, dielectric slab 714 has a thickness ofabout 10 nm to about 20 nm. In an exemplary embodiment, the second andthird region comprising the MIM structure and transition portion has alength of about 1 micrometer.

In operation, the optical signal is introduced into waveguide 710through inlet 711. The optical signal is funneled between the claddinglayer and dielectric slab at the waveguide inlet. The optical signaltravels through the waveguide towards the MIM structure. The opticalsignal may be directed by total internal reflection, refractive devices,and the like. At an opposite end, in the third region, the waveguideinterfaces with the metal layer along the transition portion. Theoptical signal undergoes a change as it moves into the transitionportion. Some of the optical signal will be lost to the metal layerwhere it will disperse. Although some energy will not be transferred tothe MIM structure, the loss is insignificant because of the greatlyincreased energy transfer efficiency of the SPP device as describedabove. In an exemplary embodiment, about 70% of the optical signalstrength will be focused into the MIM structure by the transitionportion. The optical signal travels into the MIM structure and causesSPPs to be generated. In turn, the SPPs are applied to the reaction cellin the first region. In general, the energy in the waveguide encountersthe metal interface along the transition portion 710 b and sonic of theenergy propagates down the circular taper around the reaction cell 702.

In one example, light having a wavelength of about 647 nm is incident ontaper 710 b that is connected to dielectric slab 714 that is about 5 nmthick. The slab is sandwiched between two gold layers. A plasmonic fieldwith a wavelength essentially equivalent to a 120 nm ZMW diameter isgenerated. The SPPs are then applied to the reaction cell in variousfashion such as in bursts or essentially continuously. In variousembodiments, the MIM structure is positioned in close proximity to thereaction cell so the SPPs are efficiently transferred to the cell. Onewill appreciate that the SPPs reduce the amount of background noisebecause the SPPs generally will not excite materials outside thereaction cell volume unlike a laser light that typically hasaccompanying background noise issues.

The exemplary device is configured for flood illumination from an edgeof the device via inlet 711. The exemplary reaction cells areilluminated from various angles in the plane and inherent opticaluniformity results. An optional plasmonic lens may also be fabricated atthe bottom of the reaction cell to better focus the signal energy to anintegrated detector.

One will appreciate from the description herein that the plasmonicresonator device allows for flexibility in tuning. By example, as thetaper dimension is reduced, the plasmonic wavelength is reduced, thegroup velocity is proportionally reduced, and the skin depth is alsominimized (linear with the thickness). The overall Quality Factor andefficiency can then be calculated and tuned for the input wavelength andthe required plasmon frequency with a minimal insertion loss. The taper710 b may be thought of as an index waveguide with a continuouslyincreasing diameter moving upwards. The exemplary device has aninsertion loss in the reaction cell less than or equal to about 10 dB.

The chart in FIG. 38 illustrates the results when the thickness of theinsulator in the MIM structure is adjusted. The results were obtainedwith a standard MIM structure such as that shown in FIG. 33. As shown inthe chart, the plasmon wavelength and energy level may be tuned byadjusting the dimensions of the MIM structure. FIG. 38 shows the resultsof adjusting the dielectric thickness.

The plamonic excitation device has several advantages over light-basedexcitation devices. With reference to FIG. 39, for example, the reactioncell (ZMW) can be tuned to locate the fluorophore in line with thedielectric ring height. The use of plasmons for excitation also meansthat the diameter of the reaction cell can be tuned to the plasmon andchemical geometrical requirements. In contrast, conventional light-basedZMWs generally require tuning the ZMW based on the incident photonicrequirements. The reduced wavelength of the plasmons may provide for thepossibility of a reduction in the ZMW dimension. It is apparent that,with sufficient optical shielding, the incident light may be blockedfrom the reaction cell thus providing inherent gains in the detectivityand discrimination of the tag signal.

The exemplary device may be manufactured using standard semiconductortechniques. FIG. 36 is an exemplary process flow. The optical waveguidedevice 700 can be fabricated with two dielectrics. An area around thereaction cell 702 is etched away and a metal layer 712 is deposited instep c. A very thin oxide layer (plasmon dielectric slab 714) isdeposited in step d. A balance of the metal layer is added in step e.The oxide is optionally anisotropically etched and the shape is used topattern the metal plate taper in step g. An optional cladding layer 716is added and the top metal layer 712′ is added in step j.

In the exemplary structure, the reaction cell area and surroundings aregenerally formed of known materials with the exception of a very thindielectric ring that is the waveguide. The reaction cell aperture isformed in step k. One will appreciate from the description herein thatthe above method may be modified and other fabrication techniques may beused. In various embodiments, the illumination fabrication is performedas part of the monolithic growth of the reaction cells described hereinor as an intermediate layer in a hybrid assembly.

VIII. Scattering Illumination and Detection

Referring to FIG. 42, an integrated device 100 a similar to the deviceof FIG. 1 is shown. The integrated device is configured for detection ofscattering nanoparticles 101 a while undergoing synthesis by DNApolymerase via the SMRT sequencing principle. The nanoparticles, such asgold or silver particles, are coupled to dNTPs to form phospholinkanalogs. The exemplary device is formed of a high index of refractionbase substrate 103 a, such as lithium niobate, into which illuminationlight is directed, in various respects to cause dark-field illuminationor total internal reflection illumination of the top surface. The topsurface has ZMWs 102 a fabricated from a lower index of refractionmaterial 105 a, such as glass or alumina. The illumination creates thesame observation volume confinement created in regular ZMWs, but thetransparent nature of the top surface layer minimizes scattering of theincident light.

The backscattering of metallic nanoparticles is detected while they areprocessed by the enzyme. A different sized particle is conjugated toeach of the four bases. In the exemplary device, differentiation of thebases is performed by the different scattering cross sections inherentin different particle sizes (corresponds with the sixth power ofdiameter), translating to different scattering “brightness” of thedifferent bases. The bottom side of the integrated device carries anintegrated detector 120 a, such as a CCD camera, for detecting thescattered light from the ZMW. One will appreciate, therefore, thatconventional optical components (e.g. objectives, lenses, mirrors,wedges) are not needed for detection.

One will appreciate from the description herein that the materials andconfiguration of the device may vary. Other metals or alloys can serveas a base substrate for the particles. The high index of refractionsubstrate can be different materials, glasses, polymers and the like.The high refraction index material can span the entire substrate or canbe a thin layer on a carrier substrate configured as a waveguide. Thetop layer can be other materials, such as polymers or different glasses,or composite materials. The device can also be a multilayered structure,e.g., glass with an alumina coating. A thin layer can be placed betweenthe core and cladding, e.g., a glass layer to enable surfacechemistries.

Detection using the device shown in FIG. 25 may be carried out bydirecting different wavelengths to influence the scatteringcharacteristics of different nanoparticle materials. A white lightsource (e.g. xenon lamp), which would enable spectral detection, can beused. In an exemplary embodiment, various input wavelengths are gated intime, and the differentiation of detection is based on time-gateddetection.

The bottom side of the device can also carry a cladding layer, which canbe of the same or different material of the top side, to provide aspacer between the device and the detection array. An optional mask isplaced on the bottom surface to minimize crosstalk. In variousembodiments, crosstalk is corrected computationally by cross-correlatingsignals from neighboring ZMWs. If the detector is spaced at somedistance from the chip, spacer materials (e.g. solids, fluids, andgases) can be used to improve scattering light radiation efficiencies.In various embodiments, surface morphologies are built into the backside of the chip to enhance the direction of the scattering signals tothe detection unit.

Unlike fluorescence detection, the integrated device of FIG. 42generally reduces problems with respect to signal-to-noise (dyebrightness) and photodamage. The device also does not require powerfullasers, sophisticated optics, and expensive detection technologies.

It is to be understood that the above description is intended to beillustrative and not restrictive. It readily should be apparent to oneskilled in the art that various embodiments and modifications may bemade to the invention disclosed in this application without departingfrom the scope and spirit of the invention. The scope of the inventionshould, therefore, be determined not with reference to the abovedescription, but should instead be determined with reference to theappended claims, along with the full scope of equivalents to which suchclaims are entitled. In describing the invention herein, references toany element in the singular will include references to plural, and viceversa, unless it is clear from the context that this was explicitly notintended. All publications mentioned herein are cited for the purpose ofdescribing and disclosing reagents, methodologies and concepts that maybe used in connection with the present invention. Nothing herein is tobe construed as an admission that these references are prior art inrelation to the inventions described herein. Throughout the disclosurevarious patents, patent applications and publications are referenced.Unless otherwise indicated, each is incorporated herein by reference inits entirety for all purposes.

1-64. (canceled)
 65. A method for sequencing a nucleic acid comprising:providing an integrated analytical device comprising an optically opaquecladding layer having a plurality of nanoscale apertures extendingthrough the cladding layer into a transparent substrate below thecladding layer, the nanoscale apertures separated by regions of thesubstrate from any other nanoscale apertures, wherein the nanoscaleapertures each define a reaction cell for receiving a set of sequencingreagents, the sequencing reagents comprising a plurality offluorescently labeled nucleotides that differ in their excitationspectrum; a waveguide layer below the reaction cells comprising aplurality of waveguides that direct excitation illumination to thereaction cells; and a detection layer below the waveguide layercomprising a plurality of sensor elements in optical communication withthe reaction cells, wherein each reaction cell has at least one sensorelement associated with it; carrying out nucleic acid sequencingreactions in the reaction cells while illuminating the reaction cellswith excitation light of at least two different wavelengths iterativelyover time, whereby each of the at least two different wavelengths ofexcitation light correspond to the different excitation spectra of eachof the plurality of fluorescently labeled nucleotides; measuring emittedsignal over time from each reaction cell while carrying out thesequencing reactions; and correlating emitted signal measured over timewith the timing of excitation to identify the fluorescently labelednucleotide that is emitting the signal, thereby sequencing the nucleicacid.
 66. The method of claim 65 wherein the plurality of fluorescentlylabeled nucleotides comprise four fluorescently labeled nucleotides. 67.The method of claim 65 wherein a single sensor element is associatedwith each reaction cell.
 68. The method of claim 65 wherein four sensorelements are associated with each reaction cell.
 69. The method of claim65 wherein each sensor element comprises a pixel having four integratedstorage elements.
 70. The method of claim 69 wherein each of the storageelements are electronically gated by the activation of a separateexcitation source.
 71. The method of claim 69 wherein the analyticaldevice further comprises a modulated controller element coupled to boththe detector layer and the waveguide layer to synchronize illuminationand storage.
 72. The method of claim 65 wherein a delay between anexcitation event and emission for each label is preprogrammed into thesensor elements.
 73. The method of claim 65 wherein the sensor elementscomprise a CMOS, NMOS, or PMOS sensors.
 74. The method of claim 65wherein the analytical device comprises between about 1,000,000 and10,000,000 sensor elements.
 75. The method of claim 65 wherein thereaction cells comprise zero mode waveguides.
 76. The method of claim 65wherein the analytical device further comprises a fluidic conduit thatextends across multiple reaction cells.
 77. The method of claim 65wherein the analytical device further comprises a transmission layerbetween the waveguide layer and the detector layer that transmitsemitted light from the reaction cells to the detector layer.
 78. Themethod of claim 77 wherein the transmission layer comprises an opticaltunnel.
 79. The method of claim 77 wherein the transmission layercomprises optical filters.
 80. The method of claim 65 wherein theanalytical device further comprises multiple integrating nodes.
 81. Themethod of claim 80 wherein the integrating nodes are independently resetto clear previous charges from their circuits prior to transferoperations.